Aside from the doctor's crazy expression, he wasn't really that bad of a guy, I think. If he didn't have such distorted features, you'd probably think he was a half-way decent guy with a penchant for bizarre experiments. At least no one died, and everyone ends up happy.
But no one had to die. Instead, it's a bitter-sweet ending. Everyone got what they really wanted. Even though Marisa can't go back to being Marisa, she is with her child, the one she worked hard to see again. It may not be perfect, but it's close-a-freggin'-nuff.