You could try returning later, after going to another area and/or after turning in the quest to defeat Barnabus.
As you read, a couple people had trouble with the second door opening if they killed Barnabus first, when there were no opponents in the second room to kill to trigger it to open. I don't recall if the first door starts off open or closed... Anyway, at least one person returned after defeating Barnabus, doing other stuff and turning in that quest, and there were creatures in the room to kill to get the second door open.