Hi There,
I'm a longtime MainStage user and do exactly as you have described. I trigger drum samples live and in realtime from e-drum pads and clip on triggers directly connected to the input of my audio interface. NO MIDI conversion required. I'd like to offer a solution/suggesting by recommending a plugin of which I'm am part of the design and development team.
It's called apTrigga. have a look ! ... http://www.digitalelements.net/aptrigga-3-details/
There is a demo to try and see if it works for you. I'm confident you'll find exactly what you're looking for here.
** My apologies to the admins if I have stepped out of bounds .. but, this is one of the very few solutions to do this type of triggering in MainStage.