Well, you are free but total freedom is pointless really. If you could just go up to the guildmasters and say "I'm dragonborn so step aside fool" there wouldn't be much else to do!
It sure feels good to be the dragonborn though.
I think I'm talking more about whether you will play the game and strictly do as your told by NPCs in the game like Jarls, higher ranked mages, etc. Or whether you will play the game and decide to do your own thing if you don't agree with something. I do my own thing all the time, its what I love about the ES games Ive played.
Is it okay to betray a guild or rebel faction if you don't agree with the outcome in a quest like killing an innocent or handing over an artifact you don't trust people not to abuse?
EDIT: Keeping in mind that following the Winterborn Collective rules may mean no summon zombie spells (necromancy) and possibly handing over an artifact that might be used against you (I don't like such things existing, I feel threatened in the game knowing it exists and might be my undoing).