War on the Government? Sure, we could pull it off. We'll need to dig up som dirt, toss a little money around to grab their attention. Meanwhile, we could plant some sympathizers inside CAN/Autism Speaks and disassemble them from the inside. With their funds under our control, we could arm ourselves (or disassemble some other companies/programs, if the need arises) to fight against them, targetting several key areas. Better yet, we could ignore the arms and run a campaign to overthrow the government. With enough support, there would be nothing they could do but admit defeat; after all, it is the American people's right to overthrow an unjust government.
The Army wouldn't be a problem, because they aren't permitted to attack civilians. It seems unlikely that the Air Force would bomb our own territory, so we don't have that to worry about; and we could probably take control of the police department. That leaves the Marines and the FBI. It'd be tough, so we'd have to save full-scale war as an absolute last resort. Starting a war with them would only create an excuse for them to wipe us out with impunity.