Well there are ways to get layers on top of flash objects, but the flash would need to be set to wmode transparent or opaque. If only there was a way to enforce that... maybe..http://www.adobe.com/cfusion/knowledgebase/index.cfm?id=tn_15523
Then removing flash objects from the page won't be needed. Not sure if this can be made to work though, just mentioning ideas, who knows..
It's what I use to make sure my gallery pics stay on top of sifr headers. It darkens the rest of the page, I think with a transparent png or just transparency % (that's lightbox js 2.0).
**edit: After looking some things up, I think it could be possible. Shame I'm not that savvy with js or flash. All I know is that width, height and coordinates of every object can be retrieved using js, and the wmode thing should be possible to add to flash embed/objects. But then again, I don't know really much about js/flash.