I am aligned with the BoS, RR, and MM. I was disappointed to find out that I couldn't get myself kicked out of the Institute without taking on the Battle of Bunker Hill quest. I wasn't willing to go postal while visiting the Institute and turning into a mass murderer (not my style). My primary faction is the MM and I eventually completed the Nuclear Option with their assistance. The issue is the lingering state of Bunker Hill. In the Battle of Bunker Hill quest I was neutral to everyone during the firefight and simply walked into town, entered the cellar, and with freeing the runaway synths in mind I retired my courser chaperone. Naturally I used Kellogg's .44 to do it right. I like to think he would have approved. Anyway, I then checked with each of the runaways (speech engagement) as they had quest pips over their heads. They thanked me and said they would leave after me. On my way out of the settlement I decided to help eliminate as many of the Institute synth attackers as I could and quickly dispatched a dozen or so. I stopped when I discovered that the quest seemed to continued to teleport new waves of attackers indefinitely. Strange I thought and decided to make my way for my final confrontation with Father on the roof of the CIT building. I thought I was finished with Bunker Hill and continued the main quest line to completion.
On my first visit to Bunker Hill after destroying the Institute I was surprised to see the BoS squads standing idle outside the Hill. They make a wonderful guard of course but their presence is unwelcome and I thought strange. The fine citizens of Bunker Hill are still cowering in fear though in their respective shacks. They talk and barter but all exhibit the panic mode behavior. Visiting caravan traders have the run of the place and are acting normally. The original runaway synths and their RR heavy protectors are still hanging out in the basemant though. I read on the wiki that newly escaped synths will also head to the Bunker Hill basemant for processing when completing the new radiant RR quests but why are the originals still there, why hasn't the BoS gone home, and why are my settlers hiding in their shacks?