There are plenty of easy ways to handle this. As Jurij pointed out, when a PC is actively using their gang, you have to spend the bullets and pay for their food/water for the day. If the gang is just doing other work for the Boss in the Ark, he don't have to pay for the gang. If spending 13 food/water per day isn't a problem for the Boss, then you may be handling the scarcity of resources in your game wrong (see rule #2, of Chapter 9, "Your Job As Gamemaster")
But in this case, if the PC does want to actively use them, and he takes all his men with them, you can use other methods to balance it out. It would be easy to have another NPC break into the PC Boss' Den and steal stuff (leaving your turf unguarded = bad idea). I've seldom had a boss bring his ENTIRE gang, except in rare "showdown" type situations. And if this is a problem, then give another Boss in the Ark the same talents and/or an even higher Command (i.e. bigger gang). The GM has ultimate say over NPCs and their actions.
And if the PC Boss isn't phased by all this, and they do want to bring 12 gunmen with them and pay for them all, remember that the GM handles all the NPC's actions. If they're not involving PCs, then you completely decide the results (e.g they miss every shot, cross off 12 bullets for that round, Boss). If they are shooting another PC in the group, then you really have bigger GM problems. Even then, if they fail their Shoot roll, maybe their gun jams/breaks, or they shoot a fellow gang member. If the Boss really has it coming, maybe a NPC/robot/devourer shows up and kills some of this gang. Use ham-fisted actions like this sparingly and only when players are behaving badly. You don't want the game to get confrontational (PCs vs GM).
And remember that the golden rule of all RPGs is that the game should be FUN! If you have players who are not having fun, then the game is probably in trouble. Whether you do it in game, or out-of-character, the GM needs to get things back in line.