Quick answer... Using AS3, no.
You cannot manipulate the media before it hits the FlashPlayer neither you can change it after it is processed.
Although you have two possible choices:
Process the sound sent from Flash Player on the server side and try to improve it there.
Change the technology from Flash to WebRTC and try the acoustic echo cancellation provided by the browsers. It will only work on Chrome and Firefox for now, but it may be the future replacement of Flash. If you still don't like the level of cancellation, you can also process it on the server side because, just like Flash, you cannot mess with the stream on the client side in real-time.