After playing with it for a short while, my preference would be that track mute mutes the entire track including CCs. CC sending is a really cool feature but it takes too long to go through check all modulators on all tracks, turning off any that are modulating a CC. You need to be able to quickly mute stuff imho.
I think the fear of sudden jumps is unnecessary. Sudden jumps might already be part of your modulation - and it's how CCs work generally, so shouldn't worry too many people.
Anyway, it's a great addition thanks for doing it! Will be driving my Minilogue XD crazy the rest of the afternoon!
P.S. Could I suggest holding Set and the relevant Mute button toggles between the button muting notes, notes & CCs and maybe even just CCs? If the button is also RGB it could have a colour for each of the mute types. I think muting just CCs will be handy because, sometimes when you have several modulations running, it's hard to know which is doing what. Being able to quickly mute in this way would really help keep track of what's what.