I still don't see why T3 had to be in that fight in the first place.
I hate this example, because then people bash T3 to try and make their argument better. But you're right, he's freaking awesome, he's been upgraded so many times.... like really, what astromech droid has a built-in blaster? He even challenged the Sith Emporer! Then died like 2 seconds into the battle....
Anyways, if you want to be technical about it, the HKs used flamethrowers against him, which have never historically been super great against droids. One of the drops from that battle is also a matrix that gives a boost to droids when attacking "biologicals". So they were obviously designed to kill living things (which Traya's assassins are) rather than droids like T3.
But anyway, I see your point on the programming.
The same way she gets them on the planet I suppose. Getting off the planet seems a bit hazy. It's not like she can rip ships out of the vortex like Nihilus did. I would assume that they will get off in the same manner that Sion did. Unless he left with Nihilus.
How is she going to get them off Malachor? That's my question.
And, if she does, won't their power be far less, seeing as they aren't drawing from the dark side nexus?
Well, it's not like they are powerless off Malachor. But they are less so when away from Malachor. I wouldn't say that they are completely inept off of Malachor, just not as effective when on Malachor. I guess they would be comparable to the average Sith Warrior.