I am using Wowza Media Server 3 and Cisco TCS v5.2 Build 3222 and have had no issues. I have had the integration in production since WMS 2.2 and TCS 4... You would set it up using the guide mentioned above with any live WMV support through the built in streaming server on TCS. H.264 content will be streamed using the Wowza Media Server and from there it is playable on most devices as long as you have a player. Have you not upgraded to the most current version of TCS?
Why do you need/want Wowza to transcode WMV into something else live? From TCS you can output to live Flash H.264 to Wowza, live QuickTime to QuickTime Server or out to another WM streaming server. You could also use Cisco’s MXE3500 Transcoding engine to capture the live WMV from TCS and transcode to a MPEG-TS if needed for digital signage or IPTV devices that require that format.
My environment is TCS, Wowza(s) 3.0, Show and Share(s), MXE3500(s), and Digital Media Manager(s) with DMPs.