I have an idea, not sure if it might work though.
Could it be possible to create a new kind of Marine or Crew member? That can only be used on Scourge ships?
Say you have a scourge ship, and you have an infestor cannon or something of a disease spreading weapon, when fired upon a ships hull there is a chance that it will infect some of the crew and marines, so when you win, you will not only get the cargo but also some extra hands to help build the Scourge fleet.
Another way is by having infected/infested marines, when you collide or kamikaze another ship, some of your marines make it on board, and start to infect/infest the crew and marines on board that ship and have a 30% chance of taking over the ship mid battle.
I know it is a BIG long shot but it would be an interesting mechanic because the battles involving these Creatures/monsters/Specimens would require you to put a lot more thinking into it when it comes to large scale battlefields.
Like if you think an enemy ship has an infestor cannon, it could take over your cruiser but if they don't you have lost a lot of firepower and that could mean the tide of the battle is not in your favor.