I think you could make the argument that women are served if men are given free contraception to use on those same women (of course -- sadly -- you have to put it in a "beneficial to women" context, but this will achieve your goal). Call them back and ask who was responsible for making that decision. Then contact whoever that person is, and point out the benefit to girls of giving free condoms to boys (or if you want, say "women/men" instead of "girls/boys").
If that person refuses to change the policy, ascertain their reasoning (they'll almost certainly have some sort of excuse), and learn if there is anyone else higher on the "blame food chain" that you can approach with this issue. You may think of this as going through the motions, but in reality you are building legitimacy for taking your case to the media. You have to show that you have done the investigatory work yourself, rather than being some disempowered and bitter parent who doesn't know what to do.
When you've gone as high up the food chain as possible and all the decision makers still refuse to alter this policy, call your local television station and ask to speak to someone in their newsroom. Get a name, and if possible, try to arrange an in-person meeting. Don't "cast your net" widely across all media outlets in your area; just pour your energy into a specific human reporter. Identify the key issues in play here (public health, stewardship of public funds, sex-based discrimination), and be prepared to give the reporter a typewritten chronology of this whole drama, along with the names and phone numbers of the decision makers that you spoke to.
Once this one reporter decides to write on this issue, and once it is published, you now have some credibility. Likely other local reporters will also be interested, and you will want to make yourself available to them. Just make sure you concentrate your efforts on human beings that you actually see in person; have them meet with you and your son, and let him also tell them this story. DO NOT send out some blanket press release. The human touch wins, so make sure you talk to a single reporter first and sell them on the story idea.
Taking this approach will rapidly build momentum for your case. At that point, your local officials will start feeling the pressure and will perhaps be motivated to change the policy so that condoms are distributed to boys too. If nothing else, you will at least send a message to parents that they need to proactively approach their own kids and intervene in whatever way they deem fit, rather than assuming that their boys are being served by the school system.
Good luck! If you get any press from this, please share it here!