The Calculator was a computer but with human brains connected to it. It was reactivated by Super Mutants. The people in Vault Zero were killed or in no way able to do anything when it was reactivated. They were in cryogenic sleep (like our character in Fallout 4). Once activated it started to go through with it's pacification protocols. So it was programmed to kill all mutations and or threats like enemy soldiers.
So was it evil? No I wouldn't say that. It was just following it's program. But depending on the ending it can become "evil" depending on how you see things. One ending, I like the https://www.youtube.com/watch?v=VwvnREVigyo