One issue only, if you decide to be a soldier in the conflct, you're bound to start the MQ at some point. Could this be fixed somehow?
Well all of the current options already silently start the MQ. The civil war stuff is also tied in pretty strongly, but on my first play through the game I was able to complete it long before I had advanced the MQ much past the initial dragon attack at Whiterun. So the MQ won't block you from finishing the war, but the war can block you from finishing the MQ. That's where the peace conference scene comes from.
Anyway, and people, please, don't get your hopes up too high on this, I have been seriously mulling over the idea of shifting goals here and turning this into a full blown MQ avoidance mechanism to start the game with. Meaning I'd be looking at
not destroying Helgen, and the only stages of the MQ that would fire would be those absolutely necessary to get the game to allow you to begin playing. the plan here would be to have the MQ initiate upon showing up in the woods near Helgen, getting caught, and then triggering the MQ proper from there. Complete with being dragged through Helgen in a slightly modified way, necessary to safeguard your gear long enough to escape your execution.
It would be a lot of work, and I have no idea what kind of consequences it would have on the world as a whole. I get that there's already a mod for this, but with as much as there is that's tied to it, I wonder just how thorough the job was at preventing it.
It also may not be the least bit feasible for civil war involvement if events there are intended to trigger the MQ through some unknown back door.