You might try putting some Javascript in the .html file that sends the current size in pixels to the flash movie. The flash movie would use this to caluclate the size at which it should display the image.
For example, the Flash movie is normally 400 by 400 pixels, and it is being displayed at 500 by 600. The Javascript takes this information (The best I can think of is to have the javascript calculate the size based on the window size. I'm not very good with javascript, so there might be a better way.) and sends it to the flash movie. Now, the flash movie's aspect ratio is being maintained, so it just passes the smaller of the two values, 500. The flash movie takes the 500, and because it is being displayed at 5/4 times its normal size, it squashes the image to 4/5 its normal size to compensate.
But this becomes pretty convoluted. A simpler solution might be layering it in the .html like oldnewbie suggested.