Exactly as JimSim831 says simply set up another profile for a controller you want to disable but with nothing assigned to it. I do exactly this so I can switch between a Logitech G940 stick for helicopters and my Warthog stick for everything else. Likewise I do the same with my Virpil collective works just fine.
Now if Asobo could allow us to set specifically which profiles to use with which aircraft then that would really enhance the sim in this respect.