I was thinking about the civil war quest and how you chose a side depending on your character well what if you could for all the quest's were its possible.
Such as:
Joining the silverhand and killing the companions guild
Helping in the rithen guard eliminate the theifs guild and restore order
Embracing alduin and help with the end of the world thing
you get the idea

Nope. I don't think a questline helping Alduin enslave mankind would be very ... logical. I wouldn't have minded destroying the Thieves Guid, though.

Not really
-riften is under the control of Maven, and as long as she is i ncontrol, the guards of riften wont ever try to actualyl stop the guild
-You cant side with Alduin becuase there would be no game after it, its like siding with Dagon, it owuld just mean game over

Also, the entire point of the thives guild is that before you start the questline, they dont really have any power anymore. You cant destory something that is effectivly dead.

yup its like they have a prophecy of someone saving their butt

i agree about the thieves guild when you join. But the talk around the rest of skyrim sort of points towards its a shady place because of them even in a weakened state. You could become a dragon priest of your very own just like the good old days.