This, I think, is just as old a debate as the whole Sci-Fi in Fantasy thing, and really? It's just boils down to how much peanut butter you like in your chocolate, and I'm a fan of Reese's cups!
No, really...I am, but I digress.
I've never really been a purist when it comes to my fantasy. As someone who was first introduced to RPGs through games like Crystalis and Final Fantasy, I had always just assumed a certain level of tech was A-OK, and then I started gaming, and some of the people I encountered were so strict about it, to the point where I wonder if they would consider even sighting modifications for crossbows.
And so it was that, for a very long time, unless the game was sci-fi or modern or something of a similar vein, no signs of higher tech, and especially not guns, were encountered in my playing experience.
While I didn't get to play a character in the first game I'd encountered to incorporate firearms, all that I had missed out on came to the fore when I started running a campaign set in the Forgotten Realms with a slightly advanced timeline (compared to the 3.x FRCS.)
In that campaign, a group in Lantan had gotten the breakthrough that was actual gunpowder, and swiftly began manufacturing (relatively) cheap guns, of which my pal Zack's Scout owned 2. Pistols, to be exact, which he further modified in-game to be 4-chambered revolvers.
My initial reservations mostly were with the damage output of firearms, and how, at early-to-mid levels, not only were the weapons devastating in the hands of PCs, but they could end an adventuring career quickly if the opposing team had them.
And though what I feared is most certainly true, and was almost made manifest a few times, including firearms also added a certain mystery to tech that I feel, in some cases, rivaled magic, and even if the weapons were amazingly destructive, it was tempered by the fact that my players were big boys and could handle a character death, and the simple fact that the things, while cheaper than a normal gun in the realms, was still prohibitively expensive, meaning that not everyone was toting a long tom around to supplement their swords.
The whole reason I'm even talking about this is the release of Ultimate Combat for the Pathfinder RPG, and the rules for the Gunslinger class and large list of firearms available.
Though I feel that the Gunslinger can tilt a little on the unbalanced side, I'm not one to care about that, really, and I don't see it as a fault. The abilities are well thought-out and flavorful, many of them reminiscent of spaghetti western action and tropes. They even have a "Mysterious Stranger" archetype with an ability called No Name. Classic stuff.
The weapons themselves, I have very little issues with, and while I, personally, wouldn't include all the guns provided in the weapon chapter, I certainly wouldn't balk at including a few, and perhaps conceding one or two to a player who wanted to manufacture some of the more ambitious (and powerful) weapons.
I think that guns can make a powerful and mysterious weapon for a fantasy campaign, and I embrace the chance to throw interesting things in my game to give my players something new and surprising. I'm the kind of DM that will throw Warforged Titans that can transform into Lightning Rail troop transports into my game, so yeah...
I can understand if it's not your thing, but I would recommend the Pathfinder rules for the use of firearms if you are running a game derivative of the 3.x system. It's streamlined and designed well enough that you can drop any of it into your game with little to no work on your part.