The solution is simple (it requires MM's programming, sure):
You enter the armoury, and you automatically lose your weapons, as if you just respawned unarmed. Weapons menu pops up.
Then you get to select your new (or previous) weapons, both primary and secondary. There would be no "two primaries" selected, the same way you cannot select two primaries when you respawn after killed.
Besides, if you dropped your gun before entering the armoury, that one could dissapear (so you don't stack a pile of weapons just outside it, just to go back an select new ones to stack).
I like this idea, but only in team maps like inf or ctf.