You can install a flexible coupler in the ductwork before it gets to the plenum, preferable far from the furnace so the mechanical transmission can attenuate as much as possible. You can also use ducting that is lined with absorptive material or if the ducting from the theater room can't be replaced, a baffle can be installed near the furnace. This is basically a box made of internally insulated duct material, placed at a 45 degree angle to the return and supply air ducts, and with an absorptive baffle in the middle of the box. That way, the sound is attenuated somewhat before it gets to the de-coupler, sound deadening box and baffles. HVAC people hate things like this because they like laminar air flow but this is a good time for a compromise.
If necessary, using a separate blower to maintain the temperature in the theater for fresh air will help and it would reduce the need for attenuation in the supply runs, although the flexible coupler will be needed anyway.
Isolation of the theater room from the rest of the structure is best. The diffusers shouldn't be directly open to the theater room- a flat panel with absorptive material on the backside helps, especially if it's a lot larger than the size of the duct- the sound can bounce off of the ceiling and be attenuated by the material on the backside of the panel, allowing less to enter the duct itself.