I also run both MediaPortal and WMC (for my HDHomeRun Prime). Under Win 7 you can PIN an application to the tray and activate it with the Win-# command. I have my Harmony 300i programed to trigger Win-1, Win-2 from the first 2 of the 5 buttons they have around the INPUT button. This way I start MP with a remote button and all is well... well, maybe not since running WMC can be triggered using the GUIDE and Live-TV buttons! YES, pressing either of those will start WMC. Oh, I also assigned Alt-F4 to the "0" button so I can terminate any app in focus.
Given the overlap I described above, I have NOT seen any conflict on the MENU button. Or are you talking about the GREEN button?