I'm away from my gear right now, but from what you describe as your setup, you shouldn't be having these problems, IMO.
Merely hooking up a MIDI controller shouldn't make your sound output suddenly stop working.
I use a Focusrite Saffire via Firewire to my Mac pro (running Snow), which then feed signal to Rockit 5's via balanced TRS cables, and I use an Akai MPK 49 keyboard as a MIDI controller via USB.
Definitely go to the Utilities folder in OSX, with all your gear connected to the Mac, and open "Audio MIDI setup", which should show you what you're using as an audio interface, MIDI controller, etc. IF it all appears to be correct, check your audio prefs in Logic as well.
I never had to set up anything funky to get the gear working as advertised. Maybe Lion has changed something I don't know about?
Hopefully someone else will chime in...