When you're being vectored under IFR, MSA and "company rules" don't really come into play. ATC has minimum vectoring altitudes for sectors that are laid out in a manner too complex for pilots to be acutely aware of, but they maintain minimum obstruction clearance. MSA is used for situational awareness and guidance in a lost comm situation, usually after a missed approach.
In your sim session, the PF's reaction was correct. I would do the same in the sim, though my reaction to the GPWS warning MIGHT be tempered IF I was in familiar territory AND I broke out of the clouds and was temporarily VMC during the RA maneuver.
One question I have is how soon after the GPWS Caution did the GPWS Warning sound? While you may not remember in the "heat of the moment," that is yet another indication of how dire your circumstances are with respect to imminent ground contact...