I've had no problems at all manipulating objectives and markers in the briefing.
Well, when the game starts properly (i.e. the briefing is over), the game timer starts. That is, time is 0 during the briefing, however long it lasts, and starts counting up during the game. If you pause in any way during your init script before making changes to objectives and markers, for example by starting an external script with execVM or using sleep at any time, then it will wait until the timer has started, which means it will wait until the game has started running. The easiest way to do this is to ensure that no sleeps are above the code in the init file and that, if you need to call an external file with this code in, you use call compile preprocessFileLineNumbers rather than execVM to call it. You also have to be careful of waituntils, but only if they are waiting for something that won't happen until the briefing is over.
The need to pause MP shouldn't be relevant, but I'm pretty sure it is impossible in the way that you are thinking anyway. You could mimic it, perhaps, by forcing the map to be shown for a time, which would prevent the players from doing anything else, but this wouldn't stop the mission (AI, etc) from continuing in the background. Still, totally unnecessary, so it doesn't matter ;P