My understanding is that the body in the wrecked ship was supposed to be the corpse of some other demonic entity, very similar to Count Iblis's true form, but definitely dead ever since the crash occurred. Once that body was found, Apollo and Starbuck quickly realized it was a reasonable guess that the survivor of the wreck (Iblis) and the dead entity in the wreck (the cloven-hooved demon) were probably members of the same species who had been travelling together.
Yes, I gather Iblis had used his powers to give himself a human form (or the illusion of a human form, or whatever the case may be) so that he wouldn't scare off the first humans who came along to investigate the wreckage.
I first watched that episode a couple of years ago, and I remember that I too had some doubts about just what the heck they had found inside the ship when they finally went in and looked. I believe the following link takes you to the online resource that clarified some things for me:
The Battlestar Galactica Wiki's entry on Iblis (specifically the "Mystery of the Crashed Ship" portion of that entry) cites the shooting script and actor Anne Lockhart's description of the body of a dead cloven-hoofed alien resembling a demon within the wreckage.