How about making the search options stick to the top of the screen instead (a la Twitter)?
Notice I'm scrolled down the page, but the navigation is still present at all times. This could be an issue if you already do this with navigation, but it has some good up-sides as well. Namely, you can fit a lot more data into a horizontal bar due to dropdowns. Since its thin and horizontal, this keeps all browser heights happy (maybe not widths, but using icons cleverly on smaller devices this could still work).
Also, I'm rather wary of trying to fit large amounts of data into small areas, like an accordion. This DOES have its place and can be useful, but we used something similar at my job and it turned into a horrid UX mess.
Based on previous experience here, I'd suggest instead of trying to cope with large filtering options, see what really get used and are necessary. You might find you can pare it down to 2 or 3 options that are useful, rather than 500 that no one uses. One key principle of UX is to keep options at a minimum so the user is not overwhelmed. This seems like a perfect example of a time to do that (unless, of course, your usage warrants it).