There's a vocal minority of fans who consider the movie to be a separate canon than the show. Beyond that, there doesn't seem to be all that much interest, except when fen deliberately set out to debate what's canon just for the hell of it, over whether the comics or canon or not, so there hasn't been the need for a consensus to emerge. I think Joss thinks they are canon, so there's an authorial intent debate simmering under the surface as well.

I'd accept Magic!Carpet!River and House!Kaylee as a sort of AU. I don't usually read that type of AU, but when it's on the screen played by the original actors that is a whole different type of story.