As I can see your problem, I have a question like why dont you use iOS streaming avaialble in FMS4.5 onwards: http://help.adobe.com/en_US/flashmediaserver/devguide/WSeb6b7485f9649bf23d103e5512e08f3a33 8-8000.html
Not sure, if you are not inerested in HLS streaming for a particular reason.
I can use that one, but it doesn't support the audio published with flash player (browser) or does it?
I mean if someone is publishing using a webcam and audio, the wrong audio codec is published, something like speex while the media serevr can only handle AAC.
Using FP, currently you can't send audio to ios devices, but after h.264 support in FP from 11.0 onwards, video can be send.
Why dont you try FMLE that can publish h.264 and AAC audio to FMS and from there it can be received to your ios client.
The question i think is, if audio and video is send using FP in a stream, so another instance of FP can receive this stream, can at the same time an ios device receive the same stream without audio?