Hi Chris,
You can embed a swf in an aspx page, so the best way I've found to utilise .net security is to make a .net wrapper application with login page that redirects to the aspx page hosting your swf on successful authentication.
If you search for my username on here (or possibly the old forum at the esri.com address) you should find the.threads where this was discussed. Can't post links myself as I'm replying on my phone.
Hope this helps