Depends on just how evil the game asks me to be, but for the most part, absolutely. I'm just never comfortable being evil, unless I can rationalize at least some antiheroic implications.
Takes City of Villains, for instance. The most evil of my characters are simply amoral. At least half my villains (including three of my six Masterminds) are going to start jumping ship the instant Going Rogue comes online. I don't usually have trouble doing newspaper missions, since thefts and spying don't get to me (and Mayhem missions are a pragmatic necessity), and I can rationalize kidnappings as disguised rescue missions (since you're usually grabbing them from other villain groups). That's usually the case.
I tell you, though, if given the ability to kill any one NPC, I suspect I'd have to wait in line for a shot at Westin Phipps. The man who has you poison the food supply of a group of refugees and homeless people, who then laughs about some woman coming to him (since he's supposedly a care worker) and crying about her little girl going blind.
...I'd be very surprised if there weren't some Architect missions that let me do that. I'll go check.