The crew on Hateful Shark was killed. One was killed in melee and the remaining four were killed by fire from three different ships in one turn. Excellent use of grapeshot! So when you transferred off, you kept control of the ship and the points for the capture. Had there been even one prisoner crew square at that point, they would've retaken the ship and you would've lost the points for capturing her. And that's still a possibility if a pirate ship grapples/fouls her.

On prioritizing repairs over other things, Electro posted a good summary of the process. You can set your HDT to something high so the ship won't fire (which will allow repairs if the other requirements are met), but there's no way to stop reloading. Since reloading also prevents repairs, it could take an extra turn or two to start repairing if both broadsides were fired.