You don't have to keep the research stations. I think it requires six. Just build six, research a couple techs, than dismantle your stations.
That doesn't cut it, and I think you can see that's one very forceful and ackward playing. Build up research, rush the tech, destroy the station ... that doesn't feel right. Plus it's not THAT easy, consider the cost of these station doing a rush like that probably will handicap other departments.
I think bombardment damage needs to be turned down, bombardment isnt supposed to go by quickly, its a very extended process. attacking an enemy planet should be an ordeal, it shouldnt be simple sending a mass of ships to bombard, you should need to protect your offensive fleet (something the AI never does)
I think both need to be adjusted. Maybe the planet need to have more hit point, at least triple. Like you said it should be a considerable afford, not like just pop in and dropping nuke.
Plus that AI behavior needs to change, since it doesn't matter if it's Pirate or anyone else for whatever reason, it doesn't make sense, sending in a kamikazi fleet to attack a planet.