Yeah, and that's a policy that a Year 10-style RPG could adopt aswell. Say you're playing Spider-Man, and you want to reference Gwen Stacy's death, but the Brand New Day stuff is certainly not on your priorities list. Well, fair enough. In a decision made by the player and approved by the GMs, Peter is still married to Mary Jane. Case closed.
Honestly, past events should never dictate where an RPG's going. It's about doing new stuff with the characters and pushing ahead with new storylines and a player-created status quo. That's how the original Marvel RPG worked, and that worked out for many years. Just simplify it, and stop worrying about continuity. That's never done any game any favors.