You could definitely make use of AutoHotKey. One of the program's best features is being able to hook into the... umm... keyboard hook?... and intercept key presses. Added to that the keypress intercept can be program sensitive, so it only applies an intercept when ehshell is the active window for instance.
Basically you download and install AutoHotKey, then write a little *.ahk script that remaps your keys to nothing when ehshell is the active window. It's one of the easiest things to do with the program and I can help you if you like.
Here is an example of a script that, when active, disables the keys "q,w,e,r,t,y" when notepad is the active window.
Code:
#IfWinActive, ahk_class Notepad
q::return
w::return
e::return
r::return
t::return
y::return
Download and install AutoHotKey, save the above code into a file called "testqwerty.ahk" (anything .ahk will do obviously), and double click the ahk file. You'll then get a little green H icon in your systray, and while it's running you won't be able to type qwerty into notepad. You can type it in anything else, and you can type QWERTY (uppercase) in notepad, but qwerty is blocked for notepad until you stop the script (exit in the systray H icon)
If this is what you're looking for I can help you modify this to block the keys that are annoying you when media center is active. You can also easily have the ahk script run at login, or better yet, have it run with media center's shortcut.
I'm using autohotkey at the moment to be the default application for RAR, R01, R02 etc files, so that when my wife double clicks an archived avi or mkv, Autohotkey unextracts it to a temporary location (With a green OSD to show the progress) and then opens that avi in Media Center. Works very well