visitkorea.or.kr has some information on routes and prices to Jeju.
The cheapest rates they quote are KRW 30,000 for Mokpo-Jeju and KRW 26,250 for Wando-Jeju.
So yes, Wando seems to be the cheapest option.
However, I travelled the Mokpo route in summer 2011. Back then my hostel host was able to get me a free shuttle bus from Gwangju to Mokpo.
I found this website helpful in actually producing fare prices:
I found that I could do a return sailing for 50 euros. If you look around the site you can try other operators.