I would never turn down an urgent request like that, just wipe everything down well afterwards. I have been in a similar situation and as others have said, he must have been utterly desperate to have asked you.
Put yourself in his position, and think how you would feel? Sometimes we have to care for others at least as much as ourselves, and the risk really is minimal if you don't get close and clean after him. We have wipes, sanitiser, paper towels and bin ready in our loo and would never turn anyone away.