The Threat cost of lethal attacks is in line with Starfleet values of non-violent conflict resolution, values that they do not necessarily share with the kind of enemies willing to zap 'em! However, just because this thematically it fits the rules doesn’t mean it’s the reason behind those rules, so it should not be inferred that the rules do not apply to Klingon or Cardassian enemies.
I’m fine with that.
If I ever run into a problem because the enemies can’t kill off the PCs because they have run out of Threat then I’ll see what the situation allows for. Maybe the enemies call off their attack and retreat, or allow for a cease fire, or maybe through a tremendous amount of luck all their remaining attacks are non-lethal without them noticing…