It's been a few years since I've seen the director's cut, but that's not how I remember interpreting it at the time. My take was that they *were* in the process of drowning us all because they saw us as a dangerous, warmongering species, but then called it off after seeing the lengths to which Bud had gone to save them from the bomb, and the love between him and his wife, and the self-sacrifice he had made for the "aliens" or whatever they were. It made them realize that for all of mankind's dangerous flaws, there's a lot of greatness in us too, and we were worth saving.