Ok, I have a solution that works for me, thanks to David's instructions on the thread:
http://www.logicprohelp.com/viewtopic.php?t=29331
Dave: "In Logic, go to Settings > Recording, and under "MIDI", select "Auto demix by channel if multitrack recording".
I changed my Keyboard controller channel ID to 2. My Drunk Kit defaults to channel 1.
I created two Software Instrument tracks. First one is my drum kit as channel 1 and the second track is the keyboard controller as channel 2.
While having both software instrument tracks flagged for recording, if my channel 1 track was highlighted, I could play both controllers simultaneously real-time with no contamination of inputs. If I had my channel 2 track highlighted, controller for channel ID 1 would control both track's input, while channel 2 controller would only supply input to the channel 2 track.
So for me, this is now perfect as I can jam realtime with two MIDI controllers with everything working properly, or even record a jam real-time.