Unfortunately, that's intended. If your stealth addon sets the NPC relationship to like (LI) as long as you're not seen, then my addon will prevent friendly fire. There is no way I can check, if that NPC is going to turn on you later.

However, it might be that your stealth addon sets the relationship to just neutral (NU). You should try to disable No damage to neutral NPCs the menu's relationship tab or via console command:
npc_antiff_rel_neutral 0

If you still can't kill enemies, it means the NPCs are set to like (LI), You will have to disable Player -> NPC in the menu as long as you want to use stealth. Or via console command:
npc_antiff_player 0
That way you can still prevent friendly fire between NPCs.

Thank you