I don't think there is any balance issue to making it nearly impossible to glass a non-domed colony. If you can wipe out the facilities, and reduce the conditions you remove almost any benefit to the owner. It's not a big deal and quite reasonable I think to require some sort of land action to completely finish it off. Actually if population could be used as low tech troops, then you could simply bomb the planet down to 1 Mil and then plant your own colony on top of it.
Before that though I think as someone else suggested earlier there should be a chance per turn of blockaded and rioting planets going over to the other side. Even if you didn't implement the other stuff about lack of resources causing starvation and what not.
Geoschmo