Did horse sacrifice persist in Christian Europe?

No. Evidence seems to suggest that the 1781 incident was highly irregular as the sources point towards one specific incident. There is also no corroborative evidence to suggest that there was an actual tradition in the German Order to sacrifice horses alongside Landkomture.

I investigated different avenues where horse sacrifice should have been mentioned, but in every case the death of von Waldeck is brought out as an unique event. Looking into the burial traditions of the Teutonic Order, there is no mention of horse sacrifices—though some promising articles are out of reach—nor would one expect the warriors of a socialized medieval elite to sacrifice one of the key elements of their military might to a burial ceremony when they were supposed to be humble and pious.

Case of Friedrich Kasimir

From the OP's:

Germany retained the actual sacrifice within the memory of living men. A cavalry general, Count Friedrich Kasimir Boos von Waldeck, was buried at Treves in 1781 according to the forms of the Teutonic Order; his horse was led in the procession, and the coffin having been lowered into the grave the horse was killed and thrown in upon it. (J. M. Kemble, "Horae Ferales", p. 66.)

This source, however, doesn't cite a better one. Indeed, 'Horae Ferales' is less exact in its description:

It is very remarkable that so late as the end of the eighteenth century we should find a similar custom practised among the members of a martial and Christian order of knighthood; for in 1781 Frederick Casimir was laid in his grave with his slaughtered horse.

Most of the language of 'Horae Ferales' is rather old, and Kemble's use of Teutonic is often with the emphasis on the Roman-contemporary Germanic tribes. He even emphasises the more prevalent nature of horse sacrifice in earlier times, with the 1781 event specifically highlighted as an exception:

Our most ancient forefathers attached that disgrace not to this trusty asso ciate but to that cowardly shrinking thief the wolf ; and in homely Pagan times the hound and the war-horse accompanied their master to the bright regions of the unseen world. We hear that it was an old custom in the North to bury the hero with his horse and dog.

This event is otherwise described in an English synthesis of a Russian article:

Coming down to more modern times we find that the custom of burying horses with their masters is less frequent in Wwestern Russia than in Estern Russia and Siberia; ... Among the Germans, the custom of which we have been treating seems to have died out in the time of the Karolingians, among the Slavs about the eleventh century; the Finnish and Turkic tribes of Eastern Russia continued it in some cases down to the eighteenth century ... Isolated cases of killing a horse at a funeral may be found in Western Europe, even in the eighteenth century, the last case being at the burial of General Count Boos von Waldeck in 1781, when it took place as a part of the regular ceremonial of the old Teutonic Order.¹
_{—Wardrop, 'The Use of Sledges, Boats, and Horses at Burials in Russia'}

The provided source for the ¹ here is Stramberg, "Rheinischer Antiquarius," I, vol. i. "Colbence," 1851, p.203; Tylor, "Primitive Culture," 3rd ed., vol. i, p.474. Even if this isolated case exists, that only a few mentions for this event exist indicate that it was definitely not common occurrence.

Traditions of the German Order

I've read a bit on the military of the Teutonic Order, and I don't know of a single instance of horse sacrifice from that. Further, two articles relating to burials within the lands of the Teutonic Order support this:

• the only mention of anything animal related found in burials in Latvia between the 14th and 18th centuries are bear claws (Muižnieks, 'Archaeological Evidence of 14th-18th Century Burial Practices on the Territory of Latvia');
• the mention of incorporating horse-items in burial graves in Samland is specified to have ended with the arrival of the Teutonic Order (Skvortsov and Khokhlov, 'Findings of Saddles from Archaeological Excavations in Prussian Cemetery Aleika-3 in Samland').

The Livonian Rhymed Chronicle

I was originally unable to access to articles. Access to one of these was provided by @LarsBosteen who cited the most relevant parts which I've included here:

It would appear also that the Teutonic Knights sometimes practised the local Baltic tradition of sacrificing material goods. The thirteenth century Livonian Rhymed Chronicle is extremely useful is this respect, informing us that after a successful battle with Lithuanians, members of the Order sacrificed horses and weapons to God. ... [The Chronik des Preussenlande says native Prussians] believed in a resurrection, but not correctly. They believed that as he is on earth, noble or common, poor or rich, powerful or not, just so would he be after the resurrection... it was customary after the death of a noble to bury with him his weapons and horse, servants and maids, beautiful clothes, hunting dogs, falcons,... Also with the common people everything they owned was burned, because they believed it all would rise with them and continue to serve them.
_{—Kļaviņš, 'The Ideology of Christianity and Pagan Practice among the Teutonic Knights: The Case of the Baltic Region'}

I highlighted the bold section from the above which looked the most promising. However, looking at the original Rhymed Chronicle I'm not sure it's so clear (though Kļaviņš is a lot more experienced in this than I am). A liberal translation (from my Estonian copy) of these lines (2662–2675 if I'm not mistaken) in the Livonian Rhymed Chronicle is:

_{When the battle had ceased
From horses to the ground
Stepped the brothers and their assistants.
They all rejoiced in their hearts.
In truth, their anger had passed,
For they had not lost anyone.
Jesus Christ was praised for this,
Who had been the saviour of the world.
He was worthy of great honour.
The arms and horses
Were divided equally.
God in Heaven
Was given His part.}

The original Low German reads:

_{Do des strites ende was,
do irbeizeten nider uf daz gras
die brudere und ir helfer do.
von herzen Waren sie alle vro.
durch recht vergangen was ir zorn,
sie batten niemant da verlorn.
des wart gelobet Jhesus Crist,
der al der werlde ein loser ist:
er was wol der eren wert.
beide wapen unde pfert
die teilte man gliche.
gote in himelriche
wart sin teil behalden.}

A similar moment is described near the end of the Chronicle, in lines 11984–11995. Free translation:

_{After it had gone so
the Christians all rejoiced.
Those who had fall to the Lithuanians
To be imprisoned in Courland
Were rejuvenated
And liberated from the heathen.
There heathen horses,
helms, shields, and swords were taken
and shared out equally.
God in Heaven
Was also given his share,
He had given them success.}

The original Low German:

_{Do diz was irgangen so,
die cristen wurden alto vriu,
die der Lettowen hant
gevangen hetto in Kurlant,
die wurden vrolich getrost
und von der heidenschaft irlost.
do nam man der heiden pfert,
helme, schilde undo swert
und teilten daz geliche.
gote von himelriche
wart bescheiden ouch sin teil,
der in gegeben hette heil.}

In a different location (lines 4701–4709) some opponents of the Germans describe how they want to burn horses for their gods (plural). The success of the Samlanders in the battle is described next, and their sacrifices are mentioned as now-happening in lines 4873—4876.

Further Research

One further article may still provide relevant informaton:

• Youmans, 'Rituals of Mobility and Hospitality in the Teutonic Knights'.