From my understanding of game mechanics, if you clear any dungeon (it will say "Cleared" on the map), it will reset with new baddies after 30 days of you leaving it alone by itself to think about what it did wrong. Bad dungeon!

What this means for you is after you walk out of the Barrow, in thirty days time you will make it impossible to finish several quests and bungle up the main storyline, requiring either a reload to an earlier save, starting the game over, or a simple cheat code into the console if you are on PC.
-Loth
Edit: If you want a good spot to halt the MQ (and not spawn random dragons) just turn the stone in to the quest-giver as always, but DON'T go to fight the menace that springs up directly afterwards... just go about your merry way and do whatever the hell you want.
