Hi Aaron,
I feel this is a fairly complicated question to answer. The short answer is - you do not need the proxy enabled because you do not need a webserver.
You can access Cognos directly through the primary dispatcher (http:\\<servername>:<port#>/ibmcognos/bi/v1/disp) and this allows you to bypass the webserver completely. I think this approach opens up a different can of worms for you. I believe you can make it work but it will be fairly complicated to do so without the webserver portion enabled.
Hope this helps.