You can see on Simon Peyton-Jones' Microsoft Research Profile page here that he gladly works for the great evil Microsoft. Despite that, the Haskell community has been relatively FUD free, and there has been very little suspicion of interference by Microsoft. Much of Simon's work in Microsoft has gone on to influence F#, which, yes, is a key part of the .Net/Mono offering.
Personally, i'm quite happy to see GHC and Haskell code in Fedora. I don't quite get what all the fuss is about.