How are you streaming this?
I think there's something wrong with your workflow if you're getting pillar box and interlace on the stream.
I use Telestream Wirecast, set Canvas to a Standard Def size (can be 16x9 as well) and set encoder to appropriate size. I can then record to hard drive simultaneously with same or different settings as desired. In Wirecast I set the Source Settings to Deinterlace.
For example. I'd stream Flash H.264 640x480 and record to hard drive PJPEG 640x480 (Windows) or Apple Intermediate Codec (Mac) for editing.
I can even do things like use HD source and stream at 640x360 and record to hard drive 1280x720.
From your description you don't have your encoder set properly.
http://www.telestream.net/wire-cast/overview.htm
