Last time I checked the Military is ran by the Feds. So yes they could hold you to a standard that says you can not use MJ even if it is legal and fire you for it's use without a second thought.
Get over it, it is now legal in two states. The what if's will be answered by the courts if necessary. Nothing is going to change the State law. If you are concerned about it, don't use it. Last I checked this amendment gives you the choice to use Marijuana without fear of being a criminal. Whether you choose to exercise that right is up to you.
They aren't what if, they are when. Which need to be answered before you pass a law. That procedure is a reckless way to govern. I'm not against it. Just pondering what the solutions are to these situations. Which are good questions. The National Guard is state run though, for the most part. Nothing like this has quite happened and I'm curious to see how it plays out and how it'll be handled.