I live in one of those towns where everyone in the local gov seems to be related or friends at the very least too.
It definitely doesn't make things easy if you're posing a perceived threat to them.
You can get around it, but it's going to take a lot of cajones with diplomacy. The cajones part comes in when you let them know you're doing this. If you're doing it on your own; without their tax ID number and insurance, they can't stop you. Setting up a nonprofit is like setting up any other kind of business in that you have the legal right to do so if you want to. They could keep you from using the school name in your org's name, using the kids as carrier pigeons and using the school grounds, but I found they generally won't follow through on that threat. The potential for embarrassing publicity is too great. Why
WOULDN'T they want the parents involved and helping, especially financially? Besides, the board members are elected into office; should they prove unwilling to do things for the kids, it's easy enough to vote them out of office.
When doing it on your own just be prepared for the costs; while getting an EIN is free and easy enough (I was shocked when less than a minute later the ID popped up on my screen!), the fees start adding up when you go to incorporate as a nonprofit and file as a 501(c)(3)--we could file under the "cheap" one, and that was $150. Then there's the insurance. It's definitely worth it though, especially if they aren't going to be overly helpful. If you go under their umbrella it would basically put you at their mercy. You might want to look into a PTA, I'm not sure how that works, but MichelleB is a good one to ask about that stuff.
You have to keep reassuring them that you're not up to "meddling" BUT-- if they ARE up to no good, they could be fearful that the nature of what PTOs do will uncover those unpleasant skeletons lurking in their closets.
Good Luck!