Just a couple of thoughts.
Using Star Trek '09 as a template for the residual effects from DOFP, it's clear that major things have changed in the Trek universe - Kirk's father and Spock's mother being dead, the destruction of Vulcan - and events took a different course, but in the end Kirk still joined Starfleet, met Spock and Bones, et al, and everyone ended up on the Enterprise as in the original timeline. Who's to say the events of X1 and that group of mutants wouldn't also come together in DOFP's new timeline? Sure events could change and X3 can be written out/reworked but there's no reason the original group couldn't still exist for more films.
I'm sure we'll get a FC3 set in the '80s, but how many films did McAvoy, Fassbender and Lawrence sign on for? I thought it was 3, so you may not get any more films with them after FC3. And if they want anymore films with the original cast they'd better hurry 'cos no one is getting younger! Lol I see no reason why future sequels with both casts can't work as long as the continuity issues between the films are handled, nd that's what Singer and Millar and Schuler Donner have to strive towards.
As an aside, is it possible that Bobby/Iceman might be one of the time travelers and somehow get stuck in the past with FC X-Men, thereby paving the way to joining a young Scott, Jean and Warren in the '80s and giving fans the original lineup? Probably not, but just a thought.