I think clones would go too far. I like the idea of Sinister stealing Scott and Jeans bodies and using their DNA to creat a super mutant or something, but to have clones of Scott and Jean walking around would feel like a cop out.
If they don't show Scott actually die, then maby they could show Sinister find him and kidnap him to use in his experiments. Kinda like they did with morph in TAS.
I also think they should have the Mutant Massacre in this movie. With Gambit leading them, only to reolize what they are doing and try to stop it. I think that would be a great intro for Gambit.