You call Metroid Prime a shooter?
*murders*
Ahh, but let's not get into that old debate again.
Voodoo, despite that one scene, the game is still incredibly good. You can't expect it to be amazingly serious, because, after all, it is a mix of anime and Tom Clancy. I don't see why you don't want to play such a good game. Everything has it's flaws, and I doubt that this scene really ruins the whole experience.
As for The Twin Snakes...they've re-done nearly all of the cinematic scenes for the game (3 hours total), so there's a good chance that they've fixed that up.