Mutantkind has been punked numerous times across time and space. It's happened before, it can happen again. Costly, yes, but hardly suicidal. Not quite sure why you're insisting on that tangent, though. The original point was that an X-Men/SHIELD full-time alliance would only piss off mutantkind in the long run. They'll bitterly look back at the overnight partnership and think SHIELD was prepping for war by stealing away mutantkind's high-profile players.
Oh, I know. Still, Maria Hill isn't obsessing over them. By current canonical standards, that's an epic win.