Why not start with a rifle loaded with say 2 rounds and have the shooter first engage a target with two rounds from the rifle, then transition to pistol. Word the stage description so the shooter must attempt to engage T1 with 2 rounds from his rifle and then transition to pistol. Allow any makeup shots to be done with the pistol. I say two rounds because it would be easy for the RO to quickly inspect the rifle mag for two rounds and only two rounds and know for certain that after two loud noises the chamber is empty.
I would certainly not have any sort of reholstering on the clock, that is just a recipe for disaster.
Sweat saves blood, blood saves lives, but brains saves both.