Do I understand it correctly that you want the player to hold the secondary weapon if he has only that, but the primary weapon if he has picked one up? If so, I would propose this:
1) Detect if the player has a primaryweapon or not (probably
primaryweapon player != null might work, otherwise let the script detect if the player has one of the primary weapons he could get his hands on up to that point of the mission).
2) Start the cutscene with a blackout/blackin combination that blackens the screen long enough to force the player to change to his primary weapon if the detection was positive.
3) Use the selectweapon command to force the player to change to his primary weapon, then fade in.
I hope this is of any helpful use for you