In thinking about it, there have been hints about Peter knowing more about Kate than he's let on from the beginning episode. I don't think they will have Peter becoming an evil character. Maybe they've known that Kate is involved, either by choice or by force, with some criminal group they've been looking for, but can't find. The called on Peter to recruit Neal because they know what his skills are and that he'll stop at nothing to find her. All speculation, of course.
Well done, USA. I can't think of an original show of theirs I haven't liked.