Well, you'd need some means of starting FFMPEG for each stream that is coming in to the server. I suppose you might be able to handle that with a C++ access plugin, but you wouldn't have any way to monitor the FFMPEG processes directly within server side actionscript. If you wanted to monitor those FFMPEG processes via server side actionscript, you'd need to build up an external process to handle it.
As to calmchess' suggestion, yeah, I guess you could go about it that way, where you'd respond to the onPublish event, call out to PHP (or another HTTP service), and have PHP execute FFMPEG. That still leaves you sort of stuck for monitoring the FFMPEG process... might be better to use a Java application so you can keep a handle to the process open on a thread, and build up an HTTP responder for the java service to query for stats.
There's another potiential issue when using FFMPEG. If I recall correctly, the rtmp library it uses isn't capable of publishing ouput to a named instance of an FMS application, so the output would have to go to the default instance of the target application (unless you want to build FFMPEG on your own and make changes to the rtmp library to handle instance names).