They are in charge since they pay his salary. Yes, the NBA is "players'" league, but that doesn't mean franchises should just bend over and take up the rear end (with no lube).
There has to be a give and take with the relationship of management, coaches and players. Otherwise, you have a player hijack your organization (ala LeBron both times in Cleveland and Kobe in Los Angeles) and leave it is disarray once they leave/retire.
As this season proves, Kawhi and his "group" want to call the shots of when he can and can't go (with no indication he's nursing an injury). That is dangerous precedent to allow a player to make without the medical staff, coaches and organizations input.
Clearly, the Raptors are okay with all this since they think it will give them some misguided leverage in resigning him. Which we all know is extremely unlikely....