You can disable the sustain pedal function on just one channel strip in MainStage.
- Click and select the channel strip for the sound you'd like to disable sustain pedal function on.
- Click on the MIDI input tab. Under the right field/box, click on the + sign to add an input. Click the up/down arrow next to the newly added input add scroll to select 64 sustain. Then click on the output in that row, and select Filter.