In reply to Luna and Nieyli, that's a topic I'd be looking at with CCP if I make it on and if affiliation mechanics fall under this CSM's season. I'll find someone, anyone, who gets elected either way if I don't get on if/when this hits and make sure this issue is addressed.
A drop in/out system for individuals and individual corps is great and fine, and stops people having to quit corp just to experiance Fac War (unlike with w-space, you don't actually need to be in a special corp to go there and partake) but ensuring you don't have the issues of individual pilots being on opposing sides would definatly be a key area of concern. Ideally, it'll work on a system that the Alliance>Corp can set an affiliation as Luna suggests, and pilots/corps are free to join that militia, or the allied militia, at will.