So I took over Fort Independence, but I didn't use the minutemen to do this, as I would have to deal with bodies lying around the castle (this was before I found out you can move bodies). I killed the mirelurk queen and took it over, but I found that the body of the mirelurk queen and the patches of mirelurk eggs didn't go away. I removed every single egg and killed every hostile there, so I concluded that the only possible answer to getting rid of the unwanted objects was to power up Radio Freedom. The only problem is, I can't get anyone to interact with the radio. None of the companions will do it, and I just found out that settlers can't do it either! Am I screwed?
If I remember correctly, when you have completed the mission Taking Independence, and defeated the Mirelurk Queen, you don't actually ever assign someone to work on the radio.
I'm not entirely sure at what point it is after the quest (before/ after speaking to Preston, before/after powering the transmitter), but a Minuteman will automatically sit down at the radio transmitter and begin tinkering with it.
That Minuteman is an essential NPC during the quest, therefore will definitely survive the Mirelurk attack and then permanently take their place at the transmitter. This means that a random settler, Minuteman or companion cannot ever be assigned to use the transmitter.