I assume there must be something in their coding that makes it difficult - perhaps if they set a progress flag after the RP battle, you wouldn't have any way of "backing out" to switch your class or upgrade equipment before you can try again?
So if they technically can't do that, then the only way around would be to split them up to have a 'non-instanced section' in the middle, where the player *could* leave the battlefield and come back later - but if you don't need to do that, then it breaks up the dramatic tension of the cutscenes.
I do think they made a bad choice of what skills they picked for "samurai easy mode" though - it definitely needed a simple 1-2-3 combo to feel flashier. So those three skills and either the DoT or the rush attack would work well. Second Wind wasn't that useful, since you were reliant on your allies' healing skills anyway.