Hi,
indeed, if you stop Unity's time, then everything using this time reference will freeze.
the other option to to manually pause each fsm, and stop the behavior itself. It's a tricyk situation.
most frameworks provide a "Real time" option that doesn't realy on Unity's time and so isn't affected by this set time scale action. iTween has it, double check this GEO thing to see if it provides a similar way.
bye,
Jean