Regardless, what Bead said are still issues that have to be dealt with.
But as Bead said, the HK-50s can't attack you because of their self-preservation programming. If they did end up fighting, it would be against G0T0 because they recognize HK-47 essentially as their same model, and they cannot let any HK unit come to harm.
Problem being that there wouldn't be any HK-50s left because the factory is destroyed. Sure maybe we can assume there are some left on some random world that G0t0 called them from, but then this ending is really no different than the previous scenario. The HK-50s would still probably attack G0t0 before they attack HK-47.
Like Bead said, G0T0 could pretty much scramble the droids in any scenario we've placed here, but then what's to stop G0T0 from scrambling HK-47 right off the bat? That and can the HK-51s even be scrambled?
The three scenarios we have arranged at the moment would all result in HK-47 winning. That's fine and everything, but then we're totally missing out on the HK-47 gets scrambled portion. The only possible way we could ever get any HK-5X unit to attack HK-47 is if the HK-51s are hostile, but even then who's to say they'd even listen to G0T0? By then, the HK Factory will require that you kill all of the HK-51s anyways so that ending wouldn't happen anyways...
Moral of the story: It's going to be a player controlled fight. I'm not a fan of how TSLRCM would do it and it shouldn't be dictated on how HK-47 finished the droid factory, an event that is isolated and separate from Malachor.
We've considered your opinion and your advice, and took steps to make the fight more realistic, but as far as making scenes automated just because you don't like it, it's not holding much weight with me or Bead. There are other scenes in the mod which are automated, so it's not like we're 'butchering' the entire ending for you.
Plus, if all else fails, you can always make your own mod to tweak how the game ends.