The clone theory would work if they tie in Gambit with Sinister like in the comics, minus the Mutant Massacre connection.
As for a clone being responsible for Gambit's heroic moment of self-sacrifice, I think it can be looked at the same with way Jean's return in the comics with the retcon that she wasn't Phoenix. Jim Shooter and John Byrne felt the story wasn't cheapened if it was a copy who went through that moment. The idea was that it became even more powerful if even a copy had the original's propensity to do good, so I can see that being the case for Gambit as well that the clone proved he was just as heroic as the original.