I somehow messed up and got caught stealing although I wasn't trying to steal in Diamond City.

I was on a quest and my next step was to go into a building and search for something and it was locked so I had to break-in. I did something wrong and my break in attempt failed and I had to kill everyone in Diamond City.

Then I went on a couple more small quests and was sent to Sanctuary and it was fine. I talked to someone and finished the quest and suddenly everyone was attacking.

My settlers are all attacking me and McCready but we can't kill them.

I kill them and they respawn.

They sorta sit down when their health bar hits zero and then a couple of minutes later they stand up and are in perfect health again.

How should I deal with this?

They're marked as essential (for whatever reason). So you can't kill them.

If you're on PC, you can remove the essential status, but if not I'm afraid you just have to retreat. Because they aren't going to die.

So because you were caught stealing you had to murder an entire town? O.o

I really don't want to live near you, lol.