I do believe you can use sysex remote control to mute/unmute tracks. However I don't believe you can do this with the foot pedal input.
If you had foot switches that could be programmed to send sysex commands sysex remote control might do what you want IF the mute/unmute controls outgoing midi data. If this functionality works with the E-Mu, you could probably build a bank of programed switches with a microcontroller.
It should be easy to test whether or not muting a track routed to external gear turns the midi data off. If that works, it would be possible to send sysex remote commands to simulate button presses. If that works, all you would need are some foot switches to send midi sysex remote control commands.
Even if you have decided not to get an E-Mu, I might test this out and post the results.
Out of curiosity, are you committed to using foot switches?