The easiest damn solution to fix this problem is remove the tomes from them and then the speed runners will have to find other dungeons to farm off of completely. The reason for this is to preserve the amazing story line that people should be experiencing without being forced to skip the CS and in fact I'm hearing now that people are not actually getting some of the CS in the inn from these dungeons and now this just makes the whole experience ruined by speed runners if you end up in a group with them as they might never be able to view the cut-scenes.
The other solution is to just lock everyone into the cut-scene too and that will make speed runners run off to another dungeon for sure. I also think its a good idea to just remove the timer for these dungeons as people should be able to enjoy it at a decent pace instead of being rushed by a timer.