The Doctor's grin spread a little, and leaned back, setting the glass down, and gesturing for a refill. "Oh, how little you know about me. Do you really think I was doing it to protect humanity?"
He knew humanity too well. Once the spell was broken, they wouldn't let it be reconstructed easily, and some of them would be more than happy to take out revenge for every forgotten atrocity on the Master. Of course, he had no doubt the Master would find some way to get back at them, and then he'd have more of a mess on his hands, but still.
And maybe, just maybe, he was being selfish, and wanting to keep the Master all to himself. Not that he would have admitted it then, and even now, he wasn't sure he wanted to face that part of his motivations. Not in that regeneration, not at that point in time.