Okay, I figured something out that might help against the clones, but as I don't have the problem, I can't say for sure if it works.

Anyways, you can try this:
-First make a save of your storage folder so you don't loose your things if it doesn't work out.
-Then, create a folder with any name in the mod folders, and inside you create a a "scripts", inside that one a "companions" folder. So e.g. "mods/akghoan/scripts/companions/"
-Download this file: http://pastebin.com/vqXJ4T2F
and put it into the companionsfolder, name it as "recruitspawner.lua"
-Now open Starbound, take the NPCKiller and clear your ship from the NPC's. They won't respawn now.
-Then close Starbound, delete the lua file and reopen it.
-With a bit of luck, your Crew should now all respawn and hopefully without any clones.

All the file did was basically deleting the spawn function for the crew. It is everything but elegant, but maybe it works and maybe I'll find a better solution.

Anyone who has the clones problem please try it out and tell me if he had success.
Edit: seems to work, thanks for the report!