The guy then says "Jimmy Alteri ate the pill for you". Meaning, Jimmy was sacrificed for the sake of Pussy staying alive and being able to gather more information.
That doesn't exactly prove that Jimmy wasn't a rat. All that implies is that Pussy's handler knew that Tony and the rest were suspecting a rat especially when both of them got out easy, but figured Tony assumed when Jimmy went that they had got the rat and there was no need to keep fishing.
The thing is, Jimmy was asking a lot of questions about operations and not just to get in on them, he wanted very in depth details of what was going down.
