I ran into the very same issue with a site I am building right now here:
The index page will change to be the front door to the HTML version of the site built using Wordpress and the rest will be a virtual tour of the client's facility in FC. My solution was to break up the larger site into smaller groups and to upload them into separate files on the server with the links going to the Main.html file for each page. So far so good, my largest file takes no time to load and aside from a problem loading in some SWF files all is golden. If you want to see the Wordpress site go here:
If you do go this route remember that the animations will not work to transfer from section to section, you will not be able to link directly to individual states (unless you use SWFAddress to enable deep linking) and you will want to clean out each of the individual files after you break them up so you're not downloading the content from page one when you link to page two or three.
It isn't simple but it is possible with patients. Also remember to rebuild any animation & timeline changes as well as links that involve the pages/states that you are deleting or your UI will go psycho on you.