Yeah, you're allowed to do that. The ship AI usually target hardpoints though. Frankly, it's tacticaly better to disable things like weapons if you're gonna blow it up. Anyway, after playing the Death Star, I think the it's probably possible to change the firing anim to target enemy ships (while it shows the firing sequence in a video mode, you can click the mouse to switch back to real time and command you fleet). The origin wouldn't need to be changed, just the destination. It would also have to be a separate command from the 'destroy planets' button, since we'd have to change the code to fire where the player selects a target (and planets aren't selectable).