No, they cannot be captured. The way you've been doing it is the only way available.

OK, thanks for the info.

Pretty sure I remember the subject showing up somewhere in this sprawling GC3 wish list thread. I want to be able to play as a 'planet-free' civ when GC3 finally arrives, which means the game would need to support civilian population on ships and/or bases. And doing that wouldn't even need to eliminate mostly-automated starbases that simply can't be taken because they'll self-destruct if the fight is hopeless.