So I'm at the end of The Water of Life quest and I'm about to get the scientists into the Brotherhood of Steel hideout. The chick has screamed at the intercom to let her in and the door slowly opens. When the door gets to the top, she'll run inside and the sentry and guard will turn on me for some reason. I am coming back to the game after having not played for a while, so I thought that maybe I'd forgotten something.. like.. maybe I shouldn't be wearing raider armour, so I took it off.. nope, still shot at me. Is this normal? I thought BoS were neutral unless you attack them? If I follow the girl in, the quest completes but they still chase me down.

Sounds like a serious glitch to me. I have never had that happen. Maybe wait before you run after the doctor, and try talking to the BoS guards first.