And part of the reason why it's a feature is just because of how many implications there are to simply destroying a command station without taking the planet. You gain 20 AIP, and no knowledge or anything on that planet.
Unless you have the planet in supply from another planet, then you just send a science lab over and get the knowledge anyway.
I consider it a bug because the (non-Chivalric) AI shouldn't still think it controls a building it doesn't actually control.
It makes any other capturables in that system uncapturable... unless you are ready to risk losing that civ leader. I'm also with Cyborg as well. You can't undo the AI's tech unlocks, you raise the floor, and you have to spend 7 hours before you even begin to gain benefit. Sure, the benefit's great, but you have to spend 7 hours to get it. More to the point, you have to actually survive those 7 hours... ...and, I do wonder, how often does it actually cost you more AIP due to the AIP floor increasing, in a situation like this? What if you captured 10 planets that you would normally have ignored because there were no other capturables? How much does that raise the AIP floor? How much does auto-progress raise the floor while you sit around waiting for the civ leaders to tick over enough to help you out? Was it really worth all of that trouble to get to that point, all said and done?
Now, all of that said, I don't think it's all that gamebreaking. I do think it kind of makes some sense, but not really all that much. The AI still 'thinks it owns it' when it clearly does not. There should be some official christening of it as a feature, a note or something in the tooltip for the civ leader minor faction as well as for the civ leaders themselves. While we're at it, that capability can be weakened a little bit.
"Expressly liberating the civilians of the AI will result in an immediate -3 AIP change and will let the AI know that the civilian leaders are directly working with you (so they're 'officially on your side' then). If you simply free them of the AI's iron grip, they'll slowly and quietly subvert the AI as retribution, by -2 every hour instead."