>> are we sure my suggestion about using footswitches to zero midi velocity wouldn't work to "mute" tracks?
Here's another thought--switches operated via a microcontroller that selectively filter midi data.
So let's say F# on midi channel 1 has a bass drum you want to turn on and off. You could have a button that turns on and off the filtering of all F#s on channel 1.
Out of curiosity, are there other hardware sequencers that allow you to filter midi data on the fly? If so, those would probably do what you want.