Luther originally condemned the Church being involved in military conquests and advocated non-violence against Muslims

Martin Luther first wrote about the Crusades, and general armed conflict against Muslims (whom he often refers to as "Turks" given that the Ottoman Empire was the primary military force of the day), in his Explanation of the 95 Theses in 1518.

He was suspicious of the motives of the Church

Luther thought that many of the church leaders were warmongers, rather than fighting war out of injustices (bolded text in this and subsequent quotes are mine).

Many, however, even the “big wheels” in the church, now dream of nothing else than war against the Turk. They want to fight, not against iniquities, but against the lash of iniquity and thus they would oppose God who says that through that lash he himself punishes us for our iniquities because we do not punish ourselves for them.

He also argued that the Church preferred to encourage wars against Muslims rather than admit the wrongs of indulgences and give back money from that.

So much is this so that they wanted to devour the Turks and after this banish the Christians themselves to a condemnation worse than that of hell rather than remit one penny of their indulgence tax, to say nothing of upholding the wrong done to their name and body.

He thought that the church should stay within the realm of the spiritual, not the military

Luther was critical about taking up a "sword of iron" rather than a "sword of Spirit".

And that is the truest explanation of the decrees of the fathers which so strongly forbid the bearing of arms to clerics. One can see now that an angry God, observing that we choose to interpret this sword as one of iron rather than one of the Spirit and the gospel, treats us most justly when he grants the sword which we desire and takes away that which we do not desire. Because of this there never have been in the world more cruel devastations of war than those among Christians, and the holy Scriptures have hardly been more neglected than among Christians. Lo, you have the sword which you have desired. Indeed, this explanation is one which is worthy of hell.

He argued for non-violence

Luther noted that the Crusades were a common source of indulgences, but thought that participating in a war had a poor rationale for the forgiveness of sins. He argued that it was better to serve the Muslims than to "lose your soul" by taking up arms against them.

It is well known that indulgences are granted either for participating in the war against the infidels or for building churches or for some other common need of this life. But none of these reasons is so great that love is not incomparably greater, more righteous, and more reasonable. […]

Especially is this so since it is of such great importance to give aid to souls, so that the faithful should prefer to serve the Turks and be killed in body than to lose their souls.

For reference, his contemporary Thomas More criticized this position, saying that while it was all well and good to preach non-violence out of a call to holiness, the end result was that many Christian people and churches were killed, which he found unjust.

With Muslim invasions in to Europe, Luther's stance had changed to support armed resistance against Muslims, but as a secular war

Suleiman the Magnificent led a campaign into Europe in the 1520s, capturing Belgrade in 1521 and laying siege to Vienna in 1529. Luther wrote On War Against the Turk in 1528 and changed his stance to be supportive of armed conflict against Muslims.

He was still suspicious of the motives of the Church

Luther argued that the Catholic Church had the money to effectively fund a war against the Turks, but that they preferred to use the war as an excuse to tax money from commoners in Germany (and presumably other areas).

The popes have never seriously intended to wage war against the Turk; instead they used the Turkish war as a cover for their game and robbed Germany of money by means of indulgences whenever they took the notion […] If they had seriously wished to fight the Turk, the pope and the cardinals would have had enough from the pallia, annates, and other unmentionable sources of income so that they would not have needed to practice such extortion and robbery in Germany.

He still argued that the church should not be involved in military matters

If the pope and his followers were to attack the empire with the sword, as the Turk does, he should receive the same treatment as the Turk; and this is what was done to him by the army of Emperor Charles before Pavia. For there stands God’s verdict, “He that takes the sword shall perish by the sword.” I do not advise that men go to war with the Turk or the pope because of his false belief or evil life, but because of the murder and destruction which he does.

But what motivated me most of all was this: They undertook to fight against the Turk in the name of Christ, and taught and incited men to do this, as though our people were an army of Christians against the Turks, who were enemies of Christ. This is absolutely contrary to Christ’s doctrine and name […] This is the greatest of all sins and is one that no Turk commits, for Christ’s name is used for sin and shame and thus dishonored. This would be especially so if the pope and the bishops were involved in the war, for they would bring the greatest shame and dishonor to Christ’s name because they are called to fight against the devil with the word of God and with prayer, and they would be deserting their calling and office to fight with the sword against flesh and blood. They are not commanded to do this; it is forbidden.

…if I were a soldier and saw a priest’s banner in the field, or a banner of the cross, even though it was a crucifix, I should run as though the devil were chasing me; even if they won a victory, by God’s decree, I should not take any part in the booty or rejoicing.

However, Luther argued that the secular authorities should wage a war, so long as it was self-defense and not a "Crusade"

Luther argued that it was the duty of the Emperor to protect their people against the Turks who he saw as aggressors maltreating their captives.

Nevertheless, what the emperor can do for his subjects against the Turk, that he should do, so that even though he cannot entirely prevent the abomination, he may yet try to protect and rescue his subjects by checking the Turk and holding him off. To this protection the emperor should be moved not only by his bounden duty, his office, and the command of God, nor only by the unchristian and vile government that the Turk brings in, as has been said above, but also by the misery and wretchedness that comes to his subjects. They know better than I, beyond all doubt, how cruelly the Turk treats those whom he carries away captive. He treats them like cattle, dragging, towing, driving those that can go along, and killing out of hand those that cannot go, whether they are young or old.

Luther viewed the government as the "left-hand kingdom" of God (part of his "two kingdoms doctrine") and said that it could call for war, and a person would be obligated to fight in that war in obedience to God.

In the first place, if there is to be war against the Turk, it should be fought at the emperor’s command, under his banner, and in his name. Then everyone can assure his own conscience that he is obeying the ordinance of God, since we know that the emperor is our true overlord and head, and he who obeys him, in such a case, obeys God also, while he who disobeys him disobeys God also. If he dies in this obedience, he dies in a good state, and if he has previously repented and believes on Christ, he is saved.

But Luther argued that such a war should only be for self-defense, rather than for glory or increasing land.

In the second place, this banner and obedience of the emperor ought to be true and simple. The emperor should seek nothing else than simply to perform the work and duty of his office, which is to protect his subjects; and those under his banner should seek simply the work and duty of obedience. By this simplicity you should understand that there is to be no fighting of the Turk for the reasons for which the emperors and princes have heretofore been urged to war, such as the winning of great honor, glory, and wealth, the increasing of lands, or wrath and revengefulness and other things of the kind; for by these things men seek only their own self- interest, and therefore we have had no good fortune heretofore, either in fighting or planning to fight against the Turk.

Luther made it clear that he did not view the Emperor to be the head of Christendom, as had sometimes been stated in his day.

He has been urged, as head of Christendom, as protector of the Church and defender of the faith, to wipe out the faith of the Turk, and the urging and exhorting have been based on the wickedness and vice of the Turks. Not so! The emperor is not head of Christendom or protector of the Gospel or of the faith. The Church and the faith must have another protector than emperor and kings. They are usually the worst enemies of Christendom and of the faith, as Psalm 2:2 says and the Church constantly laments. With that kind of urging and exhorting things are only made worse and God is the more deeply angered, because that interferes with His honor and His work, and would ascribe it to men, which is idolatry and blasphemy.

He also condemned imposing the Christian faith on others

In particular, killing people due to their faith was something that Luther despised.

Among us there are Turks, Jews, heathen, non-Christians, all too many of them, proving it with public false doctrine and with offensive, shameful lives. Let the Turk believe and live as he will, just as one lets the papacy [i.e. Catholics] and other false Christians live. The emperor’s sword has nothing to do with the faith; it belongs to physical, worldly things, if God is not to become angry with us. If we pervert His order and throw it into confusion, He, too, becomes perverse and throws us into confusion and all misfortune, as it is written, “With the perverse thou art perverse.” We can perceive and grasp this by means of the fortune we have heretofore had against the Turk. Think of all the heartbreak and misery that have been caused by the cruciata, by the indulgences and crusading-taxes, with which Christians have been stirred up to take the sword and fight the Turk, when they ought to have been fighting the devil and unbelief with the Word and with prayer.

One of his later hymns asked for God to protect against "the murder by the Pope and Turks"

Luther's hymn "Erhalt uns, Herr, bei deinem Wort" ("Keep us, Lord, faithful to your word" or "Lord, keep us in Thy Word and Work") is thought to have been written in 1541 for a prayer service at Wittenberg following the Siege of Buda in which the Ottoman Empire captured the city. The second line includes:

und steur' des Papsts und Türken Mord

(And control the murder by the Pope and Turks)

The hymnal Geistliche Lieder titled the song a "A hymn for the children to sing against the two arch-enemies of Christ, and His Holy Church, the Pope and the Turks". However, I'm not able to find any evidence that Luther gave it that title.

So while Luther argued for the secular authorities to fight the Turks, rather than the religious authorities, he still viewed it as entirely appropriate to pray to God for deliverance from them.