My take on this is generally that the photon torpedo system is in fact automated, and that they had to open up that room for use as a result of the movie's events. Consider three possibilities:
a) Enterprise at this point is a training ship. It would make sense to have a space where the cadets could learn how to prep and launch torpedoes, sensor probes, etc. This theory has been posted widely before.
b) By this point in the film, the ship had taken significant damage. The scene where Kirk and Spock evaluate the damage on the bridge ("They knew exactly where to hit us...") suggest that some of that damage was in the area of the torpedo launchers; thus as part of their hasty repair job they defaulted back to manual loading and arming of torpedoes through the big room.
c) They only started lifting the grilles off the track right before entering the nebula, after deciding to head there. Perhaps they needed to modify the torpedoes for use in that soup, and what better place to modify them but that compartment?