Warning: Minor spoilers ahead...

So when I first started playing Fallout 4, I only used the internet for the first 20 hours just to look up perks/statistics stuff to help my gameplay and tried to avoid spoiling future story events for myself. At that time I didn't know the multiple endings were based on faction conflict (or that there even were multiple endings) and your choice in those factions. I found this out after I was officially among the ranks of the BoS and just met the RailRoad when my curiosity overcame me. This was because I saw the evident flaws in the BoS once I looked around the operations on the Prydwen, on which Maxson promoted me to Knight rank on sight because I had already done Danse's quests at the Cambridge police station. And so I did some research here and elsewhere and now know almost all of the basics to the faction conflict leading up to and about the multiple endings.
But here is my dilemna:
Once I left the Prydwen, I had already started comparing the BoS to Nazis and knew I wanted to leave, or at least weaken them somehow within the bounds on my stories' canon. And so I ignored the BoS for the most part after that (only just an hour ago seeing a BoS-manned vertibird), but when I got to the part in the story where Father sends me to assist the black Courser synth, the BoS he was fighting were not only friendly to me but also completely wrecking the Courser. So forth I resorted to killing all of the BoS present myself because the Courser seemed incompetent and near-death and because I hated the BoS, even though they wouldn't attack me because I'm technically a Knight. But this event makes me uncertain as to whether I'm stuck with the BoS and forced to ally with them in the ending, or if I can back out at one point eventually and bring down the Wehrmacht-----I mean Prydwen...?