Who cares? It's business and you do what's best for your business. I'm in sales and my top writers get special treatment, they come in a little later, get paid a higher commission and so on, if the guys who aren't as good don't like it they can quit and go somewhere else. Or they can see how the top employees get treated and strive to be there. Life isn't fair and smart business says you do what's best for the company.
In Kikos case, whether he likes it or not doesn't matter. His job is to play football, If he can't do so then Whaley has to do what's best for the team. Like you said, what precedent does is set for the team? My response is none, each instance is different an it should be treated a so. If this was Chris Hogan instead of Kiko, you drop him and move on.