To turn off aftertouch on specific channel strips in MainStage, you have to select the midi data type and then choose to filter it out. You can do this in the Midi Tab when you've clicked on the channel strip.
If you want aftertouch turn on, you have to make an adjustment at the Concert level.
- Open Sunday Keys, then click on the title at the top of the Patch List to go into Concert Level. From here, click on the Midi Tab.
- Look at the box next to "Send unassigned MIDI to all Channel Strips" and it should not be selected. It's unchecked by default because it can cause midi floods. If you'd like to enable aftertouch, you should be able to check the box and it will be passed through. You could run into performance issues, so I would definitely check this out with plenty of time to test it.