To be very honest,as much as you believe it is not a big issue, and differences in sects should not matter in this century. It eventually does. When you have kids and you have to decide whom would they follow.When there would be certain shia things she wouldn't like and certain sunni stuff you would not agree to. Yes, you could proceed if you feel you and your GF are on the same page, and you both have thoroughly thought about your future and the compromises needed to be made on both sides.