I totally agree with you, especially since the Mutant Registration Act has been brought up a bunch of times in the X books. It would make sense for them to oppose the SHRA. I know that Quesada has said something to the extent of Marvel wanting to make Civil War focus on the Avengers and not the X-Men.
Plus, as of late it seems that the US government and the X-Men are on good terms as of late, with the 198 and everything. I do beleve that the X-Men will propably be prominent and their next big event, the one that's shaping up in post World War Hulk.