A smart phone or tablet, or all of them hooked up with remote control software like unified remote is good. I also have logitech harmony link to deal with the infrared. You got everything right there, keyboard, mouse, WMC remotes, any other random remote, can even turn the computer on with a wake on lan signal. You can also customize the harmony link remote so it just has the buttons they want to use most on there. I remapped my android smart phones so harmony link is on the lock screen so its really quick to go right too it.
The other thing is if you like the harmony and they like the WMC remote why is it not OK to just let them use that, I get you dont want them to mess up with the harmony but if they have their own remote they dont need to touch it.