A public protest and advocacy are always seeking out the biggest possible venue. And when you invite patriotism into the stadium to help link your sport with goodwill toward armed services, you are going to get blowback in some form or fashion. Its inevitable and should be expected. Whether its a black armband, initials on cleats, a raised fist or boycott of an Olympics, resistance to the prevailing idea will intrude. Its part and parcel of political expression, which is what the displays are at the beginning of games. The anthem was not always played before games.
The owner can hire who they wish. But avoiding Kaepernick solely on this basis is objectively making some teams worse. There is a statistical case that Kaepernick is better than Blake Bortles, who starts for the Jags.
The risk is being overestimated.