Maybe you could specify a specific window title for your Emacs frame and use it to setup the workspace association (instead of the window class, which I assume you'd use for pidgin or xchat)
emacs --title "mu4e" -f mu4e
I don't know xmonad, but if it is not able to provide workspace associations based on windows titles, you could use a tool like wmctrl instead. For example (assuming you want to move to the desktop number 4):
wmctrl -r mu4e -t 4