And I stated multiple options for non munchkining, you don't have to worry about munchkining if you don't play the game by numbers but actually read each items description and actually stop to think about what the hell it looks like.
If your players are munchkins, as I've stated earlier, penalize them - drop some common sense and reasoning on them.
Consider other things, how well armoured are the guys they're facing? Are they going down too easily? Consider beefing them up, give the opposition at least the same capability. The door guards should be wearing some under body protection like a FFBA piece, and their clothing should also be armoured. The QRT Teams should be wearing FFBA and FBA with softweave, and your runner team should be running from them.
Armour is there in case a bit of you was sticking out of cover, or you were caught out in the open, the firepower of coordinated opposition should make standing out in the open and walking into fire a non option.
So weather it's coordinated tactics, or better equiped NPCs, or both you should be able to work it out and keep the opposition challenging and on the runner's level. As well, consider what your PCs are wearing, and how logically it should impact them.