I don't think some scenes totaling maybe 10-15 minutes of actual screen time really would affect the prison aspect - if anything, it'd just show that history is doomed to repeat itself. I mean, we had Magneto holding Kelly captive in X-Men; Deathstrike, Mutant-143, Xavier, Cyclops, and six of Xavier's students held against their will to benefit Stryker in X2; the mobile prisons in The Last Stand and then Stryker's guinea pig tanks in Wolverine - so imprisonment is a recurring theme in the movies, even if they continued that idea, it wouldn't be anything new.
That's why I'd much prefer the persecution of mutants to gradually build, so that maybe if the idea of a mutant prison is brought up again, it'd be after a movie or two of these characters fighting their way up, only to be knocked back down by bigotry and legislative bodies proposing the Mutant Registration Act (which would lead perfectly into the first film). If this film is going to really break some new ground, I'd really like to see the mutants get a fair shake of things for a while, because as a newly emerging species to hit public awareness, I don't think they should immediately be rushed at with torches and pitchforks - build up a reason for the public hatred in these films, so that we as an audience can see both sides and their viewpoints represented fairly. Should an enemy in this movie or a possible sequel screw up royally, with the whole world watching (think if Proteus had a meltdown and destroyed an entire city block because he wasn't able to control his powers), then the baseline humans will have a reason for all their anti-mutant rallies and their "rabble, rabble, rabble" cheering for Kelly in the first film.