I don't know if there is a free alternative to Flash CS, but there are free options to write and compile Actionscript, which is the programming language used in Flash. The downside is, you'll be missing out on the visual editor Flash CS has to create animations and other fancy things. Everything you can do in Flash CS however, can also be done in Actionscript, it just takes a little more work. Being a programmer myself, I prefer the pure Actionscript solution, but that's just me :)
The Flex SDK (Software Development Kit) by Adobe is free, and can be used to compile Actionscript. FlashDevelop is a free development enviroment you can use to write the code, and can be used with the Flex SDK.
Here is a link to Flex:
http://opensource.adobe.com/wiki/display/flexsdk/Flex+4And a link to FlashDevelop:
http://www.flashdevelop.org/wikidocs/in ... =Main_PageThere's also a good tutorial on the FlashDevelop site on how to get it up and running with the Flex SDK. It can be found on the site under documention, and will be presented after installing FlashDevelop.
This all assumes you're willing to learn Actionscript programming of course.