you could try to convince them to replace the iframes with <div>s.
you can make it look identical to their framed pages by using position:fixed on the sidebars and menubars so they don't scroll with the page, and add some scrollbars to the div if the content overflows.

but the css is a little buggy on older browsers. so you might not be able to get it looking perfect for everyone (you might end up with the sidebars scrolling, for example). but you can use javascript to fix that.

if they insist on leaving it as it is, then just replace all the links to the outer frame with links to the content frame instead, and use javascript to load the frame around it when people visit it direct.

... or ... if you just want an easy life ... just put all the URLs into a sitemap.xml file and link to it in your robots.txt