I don't think Joel was wrong in killing the people who were surrendering. He's been surviving in a hellscape for 20 years. It would be dumb of him to let them live as it will give them a chance to get back at him later. That was case for him and Ellie in their encounter at the university. Had he let them live they likely would have tracked them to Jackson.
The Fireflies are not a lesser evil in my eyes. From what I remember from the Riley episode the fireflies bombings would often put civilians in danger and they treat it as collateral damage. Fireflies don't have any moral objections to recruiting children. Their mission statement of wanting to restore the world to how it was is ridiculous when it's beyond repair for that goal to be realistically possible. Given how divisive they are to the general public of the setting they are not as effective as they should be.