So did Hitler............. Anyone who plans on killing mass numbers of innocent people is an evil villain. God, justice, or simple psychic rage are not good excuses to slaughter mass amounts of innocent people.
Just because it sounds good in their heads does not make it ok.
Master didn't plan on killing mass numbers of innocent people.
His plans was to turn as many into super mutants as possible, which while there was a certain mortality rate he still didn't "plan" on killing them.
And then let the rest of the humans that are alive live out their lifes under Unity control but be prohibited from procreation.
But his plans were never to just "murder everyone".