I don't think the Major has a leg to stand on.
First, between the President and the Major is a chain of command, and that chain of command determains what his orders will be. The fact is if the Major has served in the reserves, and collected just one paycheck while Obama was President, that in effect sends the message the Major recognizes Obama as Commander in Chief. Aside from that, the issue has been decided and settled, Obama was reviewed and allowed to run, and he was elected. He was sworn in, back in January by the Chief Justice of the Supreme Court, and is the Commander in Chief.
The Major is screwed, and if he wishes to stay a happy Major for long, he needs to shape up. Stopping his orders were not a result of challanging the Commander in Chief, if was a result of knowing sending the Major could result in someone else losing their life, due to a disgruntaled command leader. A Major would have a very responsible position, in charge of many below himself. You can not allow that to jeprodize the lives of many in the command below him.
As far as I'm concerned liberals may want to pin a medal on him, but I'd give him a dishonorable discharge, for refusing orders.