I definately think the notion of mutant villains gaining amnesty will rub some heroes (and governments) the wrong way. But not necessarily to the point where it would result in flat out conflict.
But when other heroes find out about the mutant council being made up of villains, that'll definately raise tensions. I'm sure at that most most heroes (not unlike most readers) will basically be waiting for this to blow up in the X-Mens face.