I agree with the author in that it's unlikely we'll get a Star Trek scenario where a single ship can continue taking hits without much consequence. In all likelihood the first hit a spacecraft takes will destroy it.

In that environment you really want as many small ships as possible - large capital ships really work against you. Any centralized command system would also be trivially easy to destroy by concentrating fire on the command ship.

A swarm of distributed ships seems much more viable in this system.

Right, but with Paxos, you could elect a new leader as soon as the old one is destroyed.