How is it "the end justifies the means", you've already done whatever "means" you want to get to the end. No skin off my nose, waste the Geth or force some mutation on people if you like; who's to say what a Shepard controlling the Reapers would do? In-fact really that would be entirely up to you.
Isn't it also true that the Control ending is the only ending which doesn't include a specific shot of the Charon Relay exploding like the others do?
So many spoiler tags. . .