So, I came across this problem when I was designing the Gear section for M.A/C.C. How do you capture the full range of what a gun brings to a fight, while still making it both affordable points wise, and balanced with the other weapons? How do you keep it fair and even, while representing everything it can do? The fact of the matter is that you can't, not without breaking reality in an interesting way. There is a reason why the gun has taken over as the weapon of choice in almost any situation. They are light (comparatively), powerful, capable of hitting at a long range, cheap, and let's not forget easy to use. Comparatively you would need to train for months to years to be half as dangerous with a sword or staff as you are the second you pick up a gun. Sure, there will be some nuance things to it that you don't get, but in short the point and click interface a gun has makes it the king of the killing fields. At least for the time being.
So, when the party is looking to take someone down, or is interested in carrying a healthy amount of firepower, why should they not use guns? I mean, beyond all the things I listed above, they're also capable of being small and easily concealable. (It is much easier to hide a .45 on you than a Longsword for instance) Really not much, at least, not in the mechanics side of things. So what are you to do as a GM? Play up the consequences.
Think of everything I just said about guns, the ease of concealment, the cost, but most of all think of the lethality. This is the thing that will spring to mind to most people when they hear the word gun. It is the equivalent of a "this shit just got real" moment in many a movie and story. When someone pulls a gun, the intent is to kill. That is the only safe assumption to make. It doesn't matter that heroes may only be shooting to wound, because most people - trained or not - are just going to assume that that person came here to kill someone. The fact they have the gun out? Means they're going to be doing it sooner.
You need to keep those things in mind when your PCs keep going for the guns no matter the situation. Guns are loud, in more ways than one. It's pretty rare for someone to scream out "He's got a knife!" and the result being wide spread panic. Walking down main street of a city, if you're carrying a sword people are going to look at you funny. Carrying a gun? You're going to get a much wider berth of people, especially if your hand is anywhere near it. I'm sure you can picture what would happen in the event that either was drawn, and the differences therein as well.
These are details many PCs forget about, but they all lead to real world consequences that you can use to help teach the PCs something about subtlety, or at least show the consequences of actions. Pull a gun, and the situation gets more real. Fire a gun, and if someone heard they are probably going to call the cops. Not to mention that the police don't tend to like dead bodies showing up in their city, and they especially don't like crazed gunmen and women going around shooting people.
That is how you balance the power a hand gun has in a system or a game. You don't have to necessarily restrict the weapon. You just have to show the consequences to the use of it. Spider-man tells us that with great power comes great responsibility, so don't be afraid to show the consequences of being irresponsible with power.