Otherwise she could be bringing back basically everything ever that was ever stolen or destroyed. In that particular case, I could actually see why Yamamoto wouldn't want to use her powers, believing that nobody should have that kind of power. He'd likely sooner want to have those powers gone, but he wouldn't kill her either, for obvious reasons.
1 would be a bad idea, since to get Aizen back to his state before he merged with the Hogyoku, she'd first have to reverse him back to him in the state of his highest evolution. And that'd be bad.