Actually, I bet this problem (respawning with pistol in hand instead of primary) appears in a ton of missions. I just noticed I get the problem in Evo (Evolution 3 MHQ Unlocked) too.
I found this code in Evo:
removeAllWeapons _player;
{player addmagazine _x} forEach pallammo;
{player addweapon _x} forEach pweapons;
player selectweapon (primaryWeapon player);
And that code will suffer from the problem too. But now, with Worldeater's code snippet, I'm pretty sure I can fix it. I modify missions to be more playable solo or with two players (plus AI) and have the players start out with a specific kit, M16A2GL (or M4GL) and M136 with 3 or 4 M136 rounds. Having the GL (M203) seems to "cause" the problem.
@Spooner, thanks for clarifying what SPON is about. I always see the items over at Armaholic but couldn't grasp what it was all about. I would probably not use your kit code in someone else's complex mission...but would probably use it in a mission I started from scratch...assuming I could understand it. I'm a total scripting noob so so many things I look at in scripts give me "WTF" moments.