It is best to think of all swf's as having a z-order of infinity. Flash is on top and there is very little which can be done to stop that. On the other hand, if you have access to the code of the SWF itself, or if you can use another swf to load your current swf, you'll be able to use a couple of different Flash commands to address the JavaScript of the page. (ExternalInterface is your best bet).
//This is what your AS code should look like:
import flash.external.ExternalInterface;
import flash.events.MouseEvent;
root.addEventListener( MouseEvent.CLICK, useExternal, true );
function useExternal( event:MouseEvent):void
{
//swfClickFunction is defined in JavaScript
ExternalInterface.call( "swfClickFunction" );
}
Unless you are able to do either of the above, Flash will "eat" your mouse events and there is nothing which can be done about that.