Oh no I sided with the Railroad, I just meant what happened when I continued my discussions and missions with them after destroying the Institute.
Also, though the game didn't make any kind of deal out of it, I felt pretty bad when I had to take out the Brotherhood, as I'd made friends there. The ones that really got to me were (SPOILERS obviously):
- Paladin Brandis, who I'd found on the Lost Patrol mission, encouraged to return to the Brotherhood, and then was involved on the attack on the Railroad and so I had to take out.
- Field Scribe Haylen, who had been really welcoming of me and who I had supported in making sure than Danse didn't get executed, but who I had no choice but to kill when attacking Cambridge Police Station. The worst was logging on to her terminal and reading her last entry where she gushed about how wonderful I was in saving Danse. I felt horrible!
I didn't feel the same sadness when taking out the Institute as I didn't really like anyone there all that much.