I think what's probable- to keep the merger discussion brief- is that the X-projects may carry on as is, especially if they're profitable and received well, which may be the case again with Deadpool. Not only would Disney or Marvel Studios be insane to try and mess with that, but imagine the temporary backlash it would garner.
Sure, hardcore folks would argue that it meant getting Deadpool in the MCU, but the first film showed that there's a formula at play here, whether with how Reynolds has portrayed the character and especially with how the films have been marketed. Disney or Marvel Studios could look at that, and this applies to other X-projects, and just say that Fox can carry on as is. Maybe provide input when they'd like to, but to fundamentally change the brand? I don't see that happening.
Some would prefer that, sure, for the sake of putting all the Marvel characters in one basket, though.