And yeah, I've always heard it was a MGS reference, but since I have not actually played that game myself, I wouldn't know. I think it had something to do with the way the legs looked behind the wall? I could be wrong.
It's definitely an MGS reference. The fact that there's a suppressor fitted for a handgun is more proof. The way the body is stashed in the wall is a reference to how players could stash bodies in places like lockers in MGS2 & 3. MGS3 itself has a direct reference to Silent Hill in the form of a poster on a wall later on in the game.