Nova-ing the star isn't IMO a guarantee of no future contact - there may be other starlines that aren't discovered yet. Also, the SuperHappies may improve their tech over time, and may find ways of no longer needing starline tech.

Also, if there are three civilizations, odds are there are a lot more. The SuperHappies have a better structure to compete and grow with whatever other galactic superpowers exist out there.

In essence, the "closed locked door" is an illusion in my mind. Not something to base strategy on. It is the kind of thing that primitive 21st century humans would think of, and not the kind of option that an advanced 26th century human should consider viable. Were I the Confessor (and by implication, that is the role we 21st century readers are supposed to play), I would zap the Engineer, because he's building a house made of straw and taunting the big bad wolf.

But in the context of the story as it stands, this option is pointless, since the commander has already made his decision. Zapping the pilot is equally pointless, unless no one else is able to move the ship. That may be a defect of the story, or it may be deliberate.