I wasn't sure I wanted to post as I don't have a huge amount of scope on the matter, but it's definatley possible.
If you have a handle to the application (if not you can get one) you can use that to disable right click within the application.
http://www.codeguru.com/forum/showthread.php?t=190440
http://support.microsoft.com/kb/318804
seems like the most helpful links, it just goes on about how you should hook and then disregard WM_RBUTTONDOWN
and WM_RBUTTONUP
.
I'll try and write up a better thing later with an example.
More links/edits
This link could be useful as it explains that you're going to need to use unmanaged c/c++ to hook using setWindowsHookEx.
http://social.msdn.microsoft.com/Forums/en-US/clr/thread/8dd657b5-647b-443b-822d-ebe03ca4033c/
Hope this helps
[EDIT]
I think this can actually be done in a C# application completely. I will post a solution tonight
[/EDIT]