I do not believe it is possible to run WAA1SRV.EXE as a service in Win2003 Server. Where I have remote webservers that do not have tech's in attendance 24/7, I have set up an autostart this way:
I created a user account with limited authority and configured the server to auto login this user on boot.
I put a reference to WAA1SRV.exe in the Programs->StartUp group so it will be started when my auto login process has run.
I enabled a Screen Saver on the server with a short timeout (5 min) and required a relogin to resume access after the screen saver comes in.
 
Should the server reboot for any reason, we will get our website back up without a person having to do anything. Granted, I am exposed for the 5 minute window while the server is rebooting when someone could gain control of the server, but server is running in a machine room with limited access.  This is my half of a loaf solution.
 
Bruce Anderson
Houston, TX