I can't help but wonder if something else is going on here.  Thomas had been remade by Shagnasty into a killing machine in TC, and then suddenly in Changes he is the same old Thomas.  We know that Justine is Nfected, is it too much of a stretch to think Thomas was also Nfected by Justine?  Maybe the whole thing is a retcon by Jim but the fact that nobody in-universe notices or comments on Thomas' sudden personality changes is disquieting.