For the record, my problem wasn't that certain scene (as I said, it at least made sense, even if the ham factor was a little higher than it should have been.) My problem was with how stupid the entire story was. It honestly felt more like a random fanfiction taken from the Internet instead of something more polished. I also wasn't a fan of how this story essentially forced the game into a mostly linear form.
I know some will quickly argue the invisible walls theory used with RPGs and even later Metroid titles, where every game, short of glitching, that appears open is set in invisible corridors as the programmers intend a game to be played a certain way. That's cool and all, but there are times where I either don't want to continue the story and go exploring somewhere else (but herp, I can't because a door is force locked) or authorization is nonsensical in some cases.
There's also the whole introduction of a key character and key plot point aiming to tug the player's emotions around 10 minutes before the credits rolled. The only time in recent memory I've seen that work is in Metal Gear Solid 4, and even then it was a bit contrived (but that's for another topic.)