In fairness, at the time he abducted Alice, all she would have known for sure was that they knew he was in Air Force custody when they saw the train wreck, and that her science teacher knew something about him. The final pieces of the puzzle that create the empathy were discovered after her abduction. She would have known the kids were interested in him, but not known enough about him to feel any persuasive empathy herself.

As for the destruction on his way out, I read it that Joe persuaded him to just leave rather than continue his rampage. That's different from making peace. At that point, he just decided to get the hell out of Dodge and wasn't terribly concerned with collateral damage. His argument would be, "I quit actively trying to kill you all, just be grateful I left."

I think the problem for some viewers is that they processed this expository information, but never really saw the impact of it. The alien's facial gestures tell us he's calming down while in contact with Joe and we surmise from the fact he begins leaving that Joe was successful in reaching him. I think what a lot of people wanted and are conditioned to expect would have been a shot of the tanks ceasing to fire, a confused military reacting with apprehension and maybe some kind of montage showing all of Joe's information being received by the alien. Abrams left a lot for the audience to connect on their own with this one.