There are loads of remote control options for MC when it comes to browsing and playing media from MC's library (Webplay, Webremote, Gizmo, My River, DLNA control points, DLNA clients), but when talking about PVR functionality I don't think there is any remote control functionality. You have to use a copy of MC on a PC.
You could use some sort of remote desktop application (I have been playing with Splashtop on an iPad to directly access and control the copy of MC that's running on the server).
A programmable remote control will indeed allow you to control the server copy of MC, it's just a substitute for a mouse and keyboard, but presumably you need to see what you're doing! So you need the PC you're controlling connected to the TV and the PC in direct line of sight of the remote control.
It seems there is a great move towards HTPCs connected to TVs, although I've always thought that it's the remote control or thin client type approach that is more forward-thinking. See
http://yabb.jriver.com/interact/index.php?topic=67671.0