OK, you have to do the Confed mission string. So, get all lovey dovey with them, release their planets, kill pirates and Rebels till you can land again and are not attacked, (making a new pilot might be easier) then you might be able to do it.
The Switch Sides mission comes later in the string after landing on a Rebel planet (try Port Oread). Some Rebels ambush you, and tell you to destroy a Confed Frigate. Do so, and get on good terms with Rebels, and bad terms with Confeds. It would be best to finish the Confed string before doing this, because you get Rebel ships after the Confed string anyway. (It's a bug, but hey.)
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