I finished the quest about Stockton's Caravan. When I returned to Covenant, all the residents and the Turrets started shooting at me, so I ran away. Will I ever be welcomed me there again, or is their anger permanent?

This should be in the Spoiler subforum...

Since you sided against the Compound, these fanatics now see you as an evil enemy and you have to put them down or avoid them forever.

Not sure if they are even worth sparring so just off them, hide their bodies (like a real murderer) and claim the pretty settlement for yourself

Unfortunately you'll have to kill all of them now. There's no way otherwise.

What happens in Covenant is the result of people like Piper who act out of fear rather than reason.

I just had the dog. It was not his fault. I realized they were gonna stay hostile so I got em' all to chase me a bit then offed em', made for a tidy settlement.

You've either gotta kill them or just never return there. If you kill them you get Covenant as a settlement though.

I did this quest again on my 3rd character last night and decided I wanted to keep the settlement so I slept for 24 hours and went back to to kill them all in their sleep but for some reason they get quite edgy and nervous like someone was after them. I went away for another 24 hours and again they was [censored]ting themselves lol, so i ran in and them back out to take them for a little run and then killed them all.

Keep the place looking tidy compared to my last previous play through.

On my first playthrough I had to get rid of them as well.. Stripped their clothes (that i gave to my future settlers) and put them in a pile behind the house. They never despawn but my settlers doesn't seem to mind the smell.