Board Thread:Skyrim/@comment-112.198.82.215-20130909130823/@comment-7153552-20130909191918

The Dark Brotherhood will take any contract, so they have the ability to cause problems for more people. Whereas the Morag Tong tends to only take "just" contracts and high-profile things of the sort. Also, something to consider Contrib 112.198, is that whether or not you personally restored the Brotherhood to the old ways it will happen. All things are written, even what appears to be a choice for you to make final isn't always final.

Assuming you decide to destroy the Brotherhood, you are told that the Penitus Oculatus recently obtained the password to the sanctuary. The correlation here is that they also obtain it in the primary quest chain of the faction. In both of version of the chain the Penitus break in and start tearing things up (you are working for the Penitus Oculatus when you destroy them). You do not see Cicero or Babette when you destroy the Brotherhood. So some of them escape and most likely make it to the Dawnstar Sanctuary, thus allowing it to be rebuild naturally without you. The factions have to move forward in the next chapter, otherwise there will be a lot of very unhappy assassins, myself included, lol.

In a final answer I would say it's a tough call. the Morag Tong have been around for a long time, and they certianly have potential to be decidedly dangerous. However, so long as they keep their morals/scrupals, the Dark Brotherhood will stay on top.