For me, that's an easy answer. It's Dwayne Bowe (he has since returned to practice, by the way). That's not a knock on Waters who is, like Bowe, a Pro Bowler. It's actually a nod to the depth the Chiefs have at guard.
Jon Asamoah is a rookie guard that has filled in well for the Chiefs this year when called upon. He comes in as an extra offensive linemen at times and has started one game when Ryan Lilja went down. The Chiefs didn't miss a beat as they put up a season-high 274 rushing yards in that game.
Here's what our offensive line expert Bewsaf had to say about that game: "For his first NFL start, Jon Asamoah looked pretty good. He is not as quick at Lilja. Can't seemingly scoop defenders from the backside with ease like Lilja. But Jon does possess a combination of quickness and power that will help this team in the future. After a review of the tape, Asamoah could probably be a solid starter right now."
It's never easy missing a Pro Bowler, especially a team leader like Waters. But if he can't go, the Chiefs have the depth to replace him, assuming Asamoah is who they go to.
That said, even without knowing the details of Waters' illness, I'd be very surprised if he weren't able to go.