There's players behind each ship. Regardless of whatever flimsy RP > Gameplay justifications there may be, if you're going to kill them at least kill them in a way that will be enjoyable for both sides.
If PvP is not the main focus here then ensure that before you shoot/kill them, whether it be done with 1 ship or 5 ships, you can ensure the moments leading up to the first shot fired will leave the player with the satisfaction of having had an enjoyable encounter as a whole.
Remember people, there's players behind each ship and character. If we start prioritising things above those players, we are simply dehumanising ourselves and demonising the game we play.