I was going to start a thread about this myself, but I see there's already one.
Personally I'd have the aliens themselves have a 'eusocial' trait, which basically makes them slave pops, like, good at resources but not at research, but actually 'enslaving' them be meaningless. Greatly reduced (or possibly no) cost for purging them. Don't join factions. Possibly a 'listless' modifier for being owned by governments who are not of the hive.
Then I'd have the hive mind government form which gives same species happiness and -ethics drift (possibly a great deal), but lacks science. You could if you wanted make the 'leader' immortal, l'm sure. Have the hive mind government give a strong negative to individualist pops they add on. Leaders could be abstracted into concepts, or left alone - I don't think at this stage that's the biggest stopper to such a project. Eventually you might want to rethink what 'influence' means to a hive, but that could be solved later, not in the initial mechanics.
I don't think at all that it's too complex for the engine or automatically too OP. There are a lot of games going within Stellaris - not everyone needs to play the ethics drift game every time, if you make other parts of the game more daunting. Tech malus has already been suggested and is obvious.
Anyway, I think there's kind of a lot more hostility to the idea than is warranted. The game is going to get more complex over time, if it survives. Concepts like this need to find their way into game.