Maybe Jimmy was a rat however I always understood that he wasn't an informer but was whacked mistakenly (although nobody knew it at the time) in place of Big Pussy. Pussy was talking to the FBI and Tony and others in the crew knew there was a leak but could not definitely identify who was the rat. I thought that in their paranoia or over-cautiousness Tony and the other Capos were looking for any reason to clip somebody if for no other reason than to put their minds at ease. Also by pointing the finger at Jimmy suspicion points away from any other member of the crew and I'm sure they were all eager to save their own lives. It has been a while since I've watched that season but I think I remember that Big Pussy and Skip discuss the Altieri hit and it is aluded to that Jimmy was not working for the FBI and Pussy felt guilty that somebody took a bullet for him.
I might be wrong (especially on the part about Skip talking w/ Pussy) but that was always my impression.