No joke...
As per the question, I'm sure it's possible. Awhile back I asked what Qhimm thought of a program that hooked to movies much in the same manner FF7Music hooks for music files, so that the 16-bit/low-res limitations would be removed. Completely ignored of course, though I'm sure you could see the aesthetic advantage of such a program. Such a program would also be able to do this by simply locating the animation files and replacing them instead with the movie. It would probably look like a hack job as the movie would look much different than the normal battle style would, but it's certainly possible.