I looked it up and it looks like the Cougars deal with the Royals is only for 2 seasons.
If they're going to become a Cubs affiliate, all I have to say is
It won't really a big deal watching the players if they're part of the Cubs system. Most of those guys will never make it to the majors with their parent club anyway. It's just that the Cougars have always been neutral in terms of the Sox/Cubs rivalry. If they make this deal, i'd imagine they'll really emphasize their relationship with the Cubs.
Quite frankly, I don't want to go there to see Cubs Cubs Cubs everywhere. That'll be a turn off to Sox fans. But, I suppose the Cougars have figured there's more to gain by luring the interest of the more numerous Cubs fans even if it means casting aside locals who root for the Sox.