No, I don't think he should be incarcerated. He should be reprimanded, and if he still refuses to stand, he can stay in the locker room until after the anthem.
As far as the constitution, again...Kaepernick is on the clock. The COTUS does not apply. But the standards set by the NFL do. And to be honest, the NFL is allowed to set its own standards, but if I don't agree with them, it is my choice not to give them revenue. Again, I am paying to see football. When a player is on the field, he is paid to entertain me. He is not paid to school me on social injustice or politics. He can do that on his own time.