Not that I have any illusions of this ever being implemented, but I think the ideal "solution" for this behavior is to change the current reward high level players get for running low level content to work as follows:

100% clear dungeon: X tomes
Finish dungeon: X/2 tomes

Word it as you wish, but basically get 2x tomes if you cleared the whole thing, or half as many if you just skipped optional spawns and rushed to the end. It would be up to whomever implemented it to decide if they want to implement such a thing by lowering the current clear reward or just adding a bonus on top if they take their time to clear.

Oh and while at it: if someone in the group is still watching a cut scene mid dungeon, don't let the group proceed into the boss fight!!!