a rationale I never totally bought which they seemed to pull out of their ass at the last minute to give her some legroom for the future.
You mean, revealing Mystique's goal was really to save Rogue? I think it was planned all along. In an interview when #200 came out, Carey said "What makes *less* sense, on the surface, is how Mystique behaves towards Rogue in this issue. There is, or there seems to be, a huge and insane contradiction. Again, I'd just say wait and see and all will eventually unfold." Plus, there were hints in as early as #203 and #204 what her true goal was.
And given what Mike Carey's said on Mystique and her relationship with Rogue in other interviews (including "I also think that her love for Rogue – which is real, despite all the things she’s done that seems to contradict it – gives her a possibility for redemption"), it'd wouldn't make any sense at all if his original storyline was just having Mystique betray the X-Men and shoot Rogue.