I've also been using Mothership's Shield Restore on unfinished Starbases to prevent them from being destroyed.
I think shields should jump from 0 to full when the SB is finished. Would be a little easier to take them down while they are still under construction.
Starbases are way too hard to take down while they are being built considering how fragile the thing is that is supposed to be building them. I'm hoping that'll change in a future update.