As I recall, In MoR, the Marauder's Map is an ancient artifact that's starting to break down a bit, so "Messers Moony, Padfoot, Wormtail, and Prongs" are not Lupin, Sirius, Peter, and James Potter under animagus-based nicknames. Unless Fred and George are wrong about the Map's origins, though being the master pranksters of the MoRniverse (and canon, for that matter) it seems likely that their judgment would be sound in this case. So, evidence that MoR!Pettigrew, et. al. are not necessarily animagi.

I'm assuming that Eliezer makes major changes to canon only when it is neccessary to make the story work and that he will exploit resultant opportunities to mock canon, other fanfiction, conspiracy theories etc. but not go out of his way to create them. Yeah, that's a big assumption. But also, there were hints. Lupin is poor so he is still a werewolf. When discussing the Weasleys' family rat story, Harry mentioned rumors that "Black deliberately tried to get a student killed during his time at Hogwarts". In canon, Black tried to trick Snape into following Lupin when the latter was about to turn during a full moon. So they knew. They still made the map (it was featured in one of the chapters, right?). Well, they didn't have to be animagi to do that, but come on, you can't take away a major aspect of their friendship and have everything else turn out exactly the same (except the teenage gay romance thing).