First of all, the answer to your question is, you can run two different processes, one as root, but they'll have to run on different ports.
That said, I would seriously recommend against running apache as root. It's simply too large and complicated to be assured of security. In addition, it's popularity makes it a target for hackers.
It'd be far better to use something to write a simple HTTP Server and run your scripts from it. Far less code to subvert. Look at the Python SimpleHTTPServer and BaseHTTPServer classes. You can extend them and have pages up and running in a dozen lines of code.