You mean because Carol has different powers compared the old Ms Marvel set? That is a bit of a problem but if I really wanted to keep the storyline of Rogue attacking Carol, they could have it as Rogue absorbing a portion of that power so only just super-strength, durability and flight instead of the energy powers. Alternatively, Rogue could not absorb Carol and instead maybe it just be Wonder Man as Carol's love interest. It gives Carol motivation to hate Rogue without repeating the coma and amnesia plots.
As for how Rogue gets introduced, we never got Rogue with the brotherhood or being villainous so I would like to see that on-screen. If they can't do it in CM2 because of too many cast, then save it for CM3 or maybe even give the Brotherhood their own movie that guest stars Captain Marvel. Sort of like how Spider-Man featured Iron Man heavily.