That's one of the things we're very much focused on fixing. While we can't go in and change every federal government website out there, we can work to ensure that the security of the platforms we are working on is tight as possible. 18F is working with a number of agencies (see https://18f.gsa.gov/dashboard/ for the full list), and our hope is that we can be a force multiplier in security best practices throughout government.
Furthermore, we take responsible disclosure very seriously, and welcome any feedback through our email (18f@gsa.gov). We should probably take this up a notch and have a dedicated security inbox that goes directly to our core security team.