Well, what I was thinking of was that I couldn't understand why they wanted their jump-drives working at that point, rather than their beams. They were winning, why try and jump?
I was trying to stage infighting on the Repulse. Admiral Koth yells at the rookie in charge for powering down the beam cannons, then he corrects the error. The intent is that the player agrees with Koth. I think I should have been more clear that the 'rookie' was acting on his own fears over the chain of command.
Now I see what you mean by special hitpoints. Without special hitpoints, the destroyer duel lasts maybe 20 seconds. I wanted to make it longer, so I adjusted the hitpoints slightly.
Interesting to note that the Diophantine has an advantage because the Orion destroyer has 3 port side beams and 2 starboard beams. ( also one in the front of the ship, but I disabled this one on the Diophantine because it was unpredictable). I can't control Alpha 1 though, disabling the turrets changes everything. Balancing is one of the most difficult things in mission making I think.
EDIT: Fixed error I created using quotations
