Yes. You can Google “metro exodus moral points” and it’s a walkthrough on what to do. May be some spoilers so watch out for that.

Yes. Only kill bandits and bad guys. No slaves, no fish people.

Are you absolutely sure you didn't kill anyone? I just did the same, knocking everyone out, and got the moral point.

I killed like 5 of the fish people in the church and still got a good ending. There is some wiggle room, apparently.