I don't think the Daredevil deal is why Fox and Marvel have a poor relationship, particularly considering how DD launched Marvel's street-level universe. It's probably more around merchandising and Fox not wanting to join the MCU.
Keep in mind that I'm not totally willing to write off FF. Ant-Man had even more dramatic changes to the source material along with a concept I considered to be an even harder sell to audiences yet I actually want to see it since it got critical acclaim.
Plus, it'll be harder for Marvel and Fox to merge universes if FF flops. I'd like to see FF turn out well and make a profit just since it would actually help Fox and Marvel work out a deal. In a perfect world, Fox would get to keep their continuity and the X-Men from both the past (Cyclops, Storm, Magneto, Psylocke, Phoenix, Xavier, Beast, Nightcrawler and Archangel) and the present (Wolverine, Deadpool, Colossus, Rogue, Iceman, Shadowcat and Gambit) would enter the MCU. Spider-Man is getting a second reboot within a decade in 2017, I don't want to see more reboots in the MCU. I'd rather see this be the FF we're stuck with and have continuity move forward rather than start from scratch all over again.
As long as these films don't turn out like The Amazing Spider-Man films which just retread the ground from the Raimi series and made Peter too much of a jerk to be likable, I'm sure there will be sequel potential.