The short answer is no, you can't protect your SWF files from being copied when they are displayed using Moodle. There are ways to make it more difficult but ultimately, anyone can install one of the many plugins for Firefox that'll circumvent any security measures that you introduce.
Basically, Flash is inherently insecure as it's very easy to download, copy and decompile (read the Actionscript code).
The only thing that I can think of, off the top of my head, is to embed your SWF files in secure PDF files. I believe that Adobe Acrobat allows you to do this from version 8 (or earlier?) onwards. The PDF would be encrypted and fairly secure but nothing's 100%!
Also, don't be conned into buying SWF Actionscript encryption applications. All they are is obfuscators which only serve to make the code more difficult to read.
A very simple security measure you can include is for the SWF to check the URL it's on before it runs the program. So if anyone downloads and copies to another location, it won't run. You can also configure it to show a copyright message and give a link to your website. But again, anyone can decompile your SWF and change the code.
If you have any further questions, please don't hesitate to contact me.