You can't do the civil war quests without being forced to help the Jarl of Whiterun with the MQ. So no, you can't just ignore the MQ. You have to ignore both the MQ and the civil war. Why they're entangled, I have no idea. Just some more crap that Todd lied about.
Skyrim is an RPG. It was marketed in a way that suggests we're able to do anything we'd like and play however we'd like. Fine, I can understand that it's impossible to allow such things.. but why do they lie about all that instead of just coming clean? It wouldn't have been nearly as bad if they had told us Skyrim isn't as free as was implied.
No. They didn't market Skyrim like it was Second Life. They marketed it like it is supposed to be an epic adventure playing the game and following the plot. You can choose your playstyle and there is a lot of leeway in what you can do questwise, but there has to be some structure.
To OP, it's one of those things where you'll just want to avoid following the order to go to the Western Watchtower to fight the dragon. Good luck.
