You don't need to modify the SWF at all, all you need to do is change the way the Flash object is coded into your HTML. It's not all THAT hard. The SWFObject gives you fairly detailed instructions on how to do it.
MS had been in the EOLAS patent squabble for some time. The initial patch release was supposed to be last winter, but it got delayed (no surprise, it's MS). I think it got pushed out early this year. Windows and IE patches people got thru Windows Update, plus new installations.
The problem that I see that could be tricky is that the Flash is embeded using Javascript. The script file actually writes the <embed> code. I'm not sure my javascript skills are good enough to change it, but I can try  .
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