Ehh.. I have some knowledge in how the pipeline for making a game works, so I can give my insight:
Q: Can they censor the scene?
A: It really depends how the game loads up the scene, and how they attempt it; If the scene is saved somewhere along the lines of an .avi, quicktime, or something of the like, yes; they can take the file and cut out (abiet half the scene) all the scenes they don't like with a program like adobe after effects without much hassle. (I'm honestly thinking that is also how they might sync the audio too.)
Q: Can they just remove it the scene entirely?
A: If they want to risk breaking the game, sure. This is mainly dependent on how well the game was coded; if it'll skip the fact that a file is missing or a catastrophic failure like a windows program requesting a busted/broken/missing .dll file. (I've seen some pretty horrible coding which did this so..)
Q: Can they censor the scene by editing the footage?
A: Very good chance of 'no'. This would require them to go into the original animation source (Probably a scene in maya, edited with 2-3 other programs for final production video), edit it there, re-render the whole thing; and then put it back into the game (Which can either be really easy or a massive pain in the butt). Which is a) expensive and b) a waste of time and resources and c) Did was the source file provided in the first place.