(NOTE: I just got the recent patch, not sure if this has been fixed, but from the notes i don't think it has)
Even had a well developed, high-pop planet you want to capture while leaving most of the buildings intact?
As of now, a little glitch lets you do it relatively easily. Damage to planet quality and loss of buildings is only calculated when you successfully capture a planet. So, bring two transports. The first one used Mass drivers and devastates the pop but (ideally) fails to conquer the planet. Then the next one goes in with either traditional warfare or mini-soldiers, rolls over the few remaining colonists, and captures the planett with most or all of its structures intact.
This should probably be fixed.