I think that scene was deliberately vague to leave it up to debate if he really was a rat or not. It certainly looks like he was from the "evidence" against him, but then again the "Mother of God/Oh God" comment could have been due to the fact that between him and Pussy, he was one the one assumed to be the rat so it's that realization dawning on him.
If you re-watch the episode with Jimmy's arrest and release,as well as the very awkward "basement" scene with Tony at his house,I think that it becomes clear that Jimmy was definitely flipped by the cops and trying to get info for his handlers. I think the whole Altieri ratting scenario was a Chase curveball to make the Big Pussy reveal more dramatic.
