I'm very conscience of valid markup as well. I came across this issue on our website when I was moving from tables to valid strict HTML 4.01. I came across an article that recommended using an external javascript so that is what I did. This also gets around the issue with Internet Explorer issue that required you to click on a flash movie to give it permission to run.
Create an external javascript (ex. initflash.js). In the initflash.js use the following:
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//intflash.js
document.write('<object type="application/x-shockwave-flash" data="yourflash.swf" width="110" height="301">');
document.write('<param name="movie" value="yourflash.swf" />');
document.write('<a href="http://www.macromedia.com/go/getflashplayer" target="_blank">');
document.write('This section requires the Macromedia Flash Player to view</a></object>');
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Then call the external javascript where you want it to appear in your html
<script src="initflash.js" type="text/javascript"></script>
This works great for me.