It was James.  When Samus began the hunt for the Deleter in earnest, there were only two real suspects left:  K.G. and James.  There was a brief cutscene in which one unidentified soldier pushed the corpse of another into lava so that it wouldn't be found.  We never see who that body actually is.  However, toward the end of the game, a soldier approaches MB and attempts to do her in.  When Samus returns to that area, the corpse of James is on the floor.