Some things are better off dead.
If you let them live, there is no ****ing way there won't be a chance of someone planning to take them all back, probably create some synthetic sharingan and rinnegan on the way with DNA modification, and doing the whole Juubi situation from the start.
So I think there are two options here:
1. You "officially" kill them, but in reality they are alive somewhere hidden.
2. You do kill them for the greater good.