I am sure that the relationship will comeback. Afterall, in the daily comic strip, Peter and MJ are still married. But they have yet to have children, which doesn't bother anyone at all. Now if Annie is carried over to the new 616 and MJ ends up raising her, then that might be a problem. But I suspect that she'll eventually be reunited with her parents once again.
You should have had an option of "NO!!!!!"
Note: This person is a Peter Parker, Hank Pym, Bruce Banner, Reed Richards and James Howlett fanboy, used to be a Steve Rogers fanboy before he turned grumpy.
I'd rather just see them hang out as friends. Watch a ball game, tour attilan, and battle the Sinister Six.
Don't like the idea. It'd be completely random and I really don't see the point.