So, as I've been playing through again, during one of the many chases from SCP-106, I ran through a new door and found myself outside SCP-096's room. Naturally, with SCP-106 on my heels I didn't have time to stop and watch the gorefest, so I did an immediate 180° and high-tailed it back down the other corridor. The scripted event, however, had started, and the audio continued to play as I ran until the scene had finished.

Returning to that chamber later on, I found that the blood was on the windows as it should be, indicating that the event had ended correctly. However, neither of the doors will open. I know that the door outside his chamber isn't supposed to open, because it's meant to force you to enter his lair and fiddle with the power controls... But the door INTO his chamber won't open either. Did I break the game's scripting yet again by running off during the event? Or am I missing something completely normal and being an idiot?

Yup, if you exit the 096 guard room before the cutscene ends it'll make it impossible to enter the room, it's not really an error on your part, it's just a bug that has yet to be fixed.

Hotfixed it a little while back: http://scpcbgame.com/forum/viewtopic.php?f=6&t=3617

Righto then. Next time I'm playing I'll just noclip through the door into 096's cell, since it'd normally be open, and then do the power switches and carry on. Cheers.