Hmm, I've managed to get the dynarec (and therefore GLES2 plugin) to stop when the Kbd Mapping Stop key is pressed. I've set Kbd Mapping Stop to code 306, which I believe translates to ctrl + backspace on the N900 keyboard.

Anyway, it all seems to work nicely, whether --nogui is specified, or whether the GTK GUI is being used, but I've literally just hacked a stop=1 line into the stopEmulation function. It works for me, but I don't think I should release the updated mupen64plus file in case I'm doing something really stupid! If anyone does want the file, I'm happy to release the URL - but bear in mind that I am literally just hacking things together!