Well, I like this idea, personally. We already have seperate Gostecks, why not weapon gfx? It would flesh out the game a bit more.
Even if that isn't the case, I would cherish two seperate weapon lists, one for blue team and one for red. Even better, maybe in the Options tab, instead of the weapons list, there could be four buttons, one red, blue, yellow and green, and each opens up a new weapon list in a seperatte window.
The seperate weapon INI idea may work, i suppose you would have to load it by typing /loadwep(Team#) (file.txt)