From the way I saw it, Batman clearly jammed the controls. As I said before, he was stopped from stopping Ra's from loading the train, and with him battling Ra's he wasnt going to be stopping it anytime soon...not to mention, for all he knew Gordon wouldnt blow the track in time. At that point, the only option was to plow the train into Wayne Towers - destroying the train and emitter completely.
It doesnt make sense for Ra's to jam the controls - a train going full speed slamming into the 'docking bay' of Wayne Tower would be demolished. The emitter wouldnt have time to work it's magic on the water maines. Hell, you saw hole long it took change the water to gas in the Narrows - several seconds at least, seconds it wouldnt have if it would have plowed into Wayne Towers.
Again, this all tying into the explanation I posted on the other page...that seems the most logical...atleast to me. Then again, plotholes in movies are hardly a rare thing.
As to who builds a monorail system without an emergency break? Thomas Wayne, it appears.