I totally agree. Only use a hyper has on a station is if your down to like 3 hardpoints that are yellow to red and you don't feel like letting your ships finish it off. But again like i said before the way things are now if you have the cash to make a SW it normally means your going to win anyway otherwise it's a waste of 2.8k cash that could be used on some other ship.
Edit: on a side note, not many people know this but you CAN repair your station if you upgrade it. So like you said before if you can somehow fend those MKII's and be able to upgrade as soon as possible or have upgraded during the attack just click on the base and the hardpoints that are repairable will be gray, just click on them and they will start to repair. It does suck cash as it repairs though. Though i guess it wouldn't matter much with that long ass timer