Really? I don't want to go into spoilers but the DB quest is reflected in the game? Becoming the head of any faction actually? Or either side of the civil war? Please tell me one quest that forces you to lose something or turns a faction against you or even an NPC against you. There are no consequences to any of your actions in this game. You can, literally, do every quest in the game in one playthrough except the Civil War which doesn't matter because both sides play out exactly the same.
People acknowledge my affiliation and rank in the College of Winterhold all the time. I have had plenty of people refer to me as the Arch-Mage of the college.
I wouldn't mind a little bit of "you can only join our guild if you meet our requirements" when it comes to guilds, but the fact of the matter is, if you're roleplaying, that shouldn't be a problem anyways. My law abiding Necro-Warrior has no desire to join the Thieves Guild or the Dark Brotherhood, and thus, I never joined those guilds with him. Why that is so hard of a concept for people to understand is beyond me, but just because you -can- do something doesn't mean you -have to-.
As far as a quest or a choice that you make that turns others against you:
1.) Paarthurnax. Either choice you make, you are turning a faction against you.
2.) Cicero v. (The Redguard man sitting on his porch - I forget his name)
3.) Dark Brotherhood "initiation" quest.
4. Saadia v. The Alik'r quest.
And you already named one in your own post with the Civil War factions.
Those are just a couple off the top of my head, because 95 hours in on one character (whom I accidentally deleted) and I still hadn't come close to touching all of the content in the game.