They may try to stop you from killing, but that just means you shouldn’t be obvious about it. Want Lex Luthor dead? Make it look like he threw himself off the top of his building or pin the death on a business rival like Morgan Edge. Have another random enemy you want to get rid of? Figure out some Mysterio-style illusion technology (I’m sure you can find something equivalent from Kryptonian tech), and make it look like The Joker or some other crazy villain is behind the murder. The Joker got away with killing thousands of people. What’s a few more murders pinned to his rap sheet?