At least on most missions. I get that there are "Full War Mode" episodes where disable is out of the question, and nobody in their right mind would leave a Borg ship in any shape to regenerate.
But pretty much all criticism toward the Federation and their "Eliminate every ship in your way" policy would be gone if disabling hostile ships would be an option. You could even encourage it by awarding Diplomacy points if you manage to fullfill the no fatalities objective during a mission.
On some missions the result should even be failure if you destroy the adversary.
I like this idea, and it would add a bit more to the scenario instead of shoot them until the blow up. Maybe even have a BOFF skill be target weapons or target engines to disable them.
Some Science officers and the Nebula (off the top of my head) have that as a skill...but it's only used to help make them blow up faster.
The way I would do it is when their health is down to about 30 percent, a button pops up you have to click to target EPS grid or something, and when you hit it, their whole energy system fails... thus disabled. It's gonna be difficult for escorts to do it with their huge DPS load though
