I've used various Covenant-fixing mods, but the two I've tried had problems. One did some stuff I felt was redundant. One is currently bugged and has to be fixed by hand. Neither does anything about the ownership of the clutter in the area.

First off, I made everything unowned. Cheaty? Probably, but I hate how everything is still owned even after you own the place. I tried to offer a way around the cheat, though.

I tried to make turrets repairable and have them still on Covenant's side when you have to fight them, but I could not figure out how exactly repairing works. Instead, I made scrapping these turrets give you all of the parts needed to make a brand new one of the same type. It seemed like the cleanest solution.

If you don't have to fight them, turrets didn't count towards your settlement defense. I fixed that, but it requires a new game to take effect. You may still want to scrap them, to be honest, because I'm not sure the repair feature works right.

Human corpses, turrets, security cameras, and the public terminal are now scrappable! They bothered me, and I couldn't find a mod to make them scrappable.

CHEATINESS WORKAROUND:
Start a new game with just the Covenant Turrets ESP in place. (A new game is required for turret defense changes to take effect)
Play until you take control of Covenant.
Swap to the main ESP. The turret change is in that ESP as well, so you don't need the old one. Less ESP clutter!

NOTE:
You should use a mod like Spring Cleaning or another mod with the cell reset bug fix to ensure you don't have the cell reset bug. I'm still not entirely sure how it works.
You'll need a mod like Homemaker or Better Settlement Beds (replacer version) if you want to scrap the beds and/or put them elsewhere. I felt that it would be redundant.
You'll need to use a scrapping mod if you want to scrap all the things there. I added only the options to scrap the bodies, turrets, security cameras, and public terminal properly.
I may have missed a thing or two. If I did, let me know!