To set MainStage so it only receives midi input that you want - you'll want to make sure that all your onscreen controls in MainStage's Layout mode have specific assignments to specific hardware. So as a best practice you should assign your keyboard, sustain pedal, mod wheel, pitch bend wheel, etc. By default most workspace items (and thus all channel strips) will be listening for midi input from source 'All', which is exactly the behavior that is undesired in your use case. Once you create specific assignments in Layout mode to the hardware you want MainStage to respond to the issue should resolve.
You can also filter out unwanted incoming MIDI messages at the concert level. To do this ensure you have the concert level selected and go to the Assignments and Mappings tab. Scroll down to the bottom of the list and select unassigned. In the bottom pane you can then uncheck "send unassigned MIDI to all channel strips".