By allowing players to kneel, they allowed politics to enter their arena. Since they allowed the players to kneel, it's highly hypocritical to allow the kneeling, but suddenly have an issue that a veteran's group wants to place an ad in the program as a "protest" to the kneeling. Either allow all differing political speech, or allow none.
As for ordering players to stand, if I was the commissioner, my response would be this: While you are on the field and on our time, there is a decorum that all players must follow during the pre-game and national anthem (similar to if your job makes you wear a uniform or behave a certain way on the job). The national anthem is played at every game to send a message that despite the fact that we are playing on different teams and rooting for different sides to win, in the grand scheme of things, we are all Americans and should be united together despite our rooting differences. I understand you may have grievances with our society and government, but the national anthem is how we are choosing to deliver our message of unity and is not the time or place for you to air your grievances. If you still have a problem with our objective, you can wait in the locker room out of the public view. However, if you choose to remain on the field during the national anthem, you will follow our decorum.