I actually liked having the remove hotfix option in CCleaner. It cleaned up about 150 mb of space. Everything is working fine on my computers, and I don't plan on ever uninstalling the hotfixes, so removing the leftover installer files is a great idea to make space.
I can understand situations where this might cause problems. Maybe another tab, system, applications, expert? Where the expert tag contains removing the hotfix, or how about cleaning multiple user accounts on one computer? or specified directories?