Hi metromixstudio!
You mute the guitar on the Focusrite MixControl application.
Open the MixCXontrol app.
Locate the input fader for your guitar.
Each input has its own fader which you can use to adjust the amount of direct signal going to your monitors. You can set the fader to zero or activate the ‘M’ button below the fader.
I can send a screenshot if you like! 
[Carlos’ advice is good too although I cannot verify if it has any effect on latency.]