Hmm. All valid points. However, there would definitely time to refine a lot of the use of the weapons. Yamamoto was handed his bat, but he had to learn to use it effectively and ultimately received a better weapon.
Jak's never fired a real gun (much like myself) but I'd imagine no one would be a perfect shot right off the bat anyway. Not to mention that there's a lot I can do with the hand guns to upgrade them for later. Now though, the most fancy thing you could use them for is hitting a target with rubber bullets. I'm not sure if Sonya would actually let a bunch of high/middle schoolers have weapons they can't use effectively and have someone get hurt fatally.
Not to mention, if I go this route then I have a lot more play with who I can get to mentor Jak. (If we're doing that). You don't have to be a professional who uses guns all the time and only in a rigid fashion to know how to work a gun. Unlike a katana. Not saying that you can't use guns professionally, but you can certainly learn through trial and error a bit better than with a katana style. You have to be shown that, and repeat various steps.
Plus, if Sonya really is going to be training them to fight, she needs to supply weapons and know her 'students' current history. She can't expect Naoto to just pull weapons out of nowhere anyway, even if his mom is an assassin. More than likely, with these 'personalized weapons' she is trying to see who all can use what. If that fails then she might have more on standby.
As for Jak taking the weapons, that will have to be something she'll have to overcome herself. She doesn't have personal issue with guns, but being handed weapons that kill someone will take a toll on anyone. She's already made the decision, and she won't back out, but growing to accept the weapons is something that I'm sad didn't really make it into the anime or manga. If you give a kid a sword, then they are told they have to use it on people, then what comes of the person?
We'll cross that bridge when we get to it, though. For now, the guns have a great amount of play for their use and I have an idea on how they're going to 'evolve' later on. Using close range weapons are a little over played right now too. Jak will deal with the idea of using the weapons as it comes, because that's how she works.