1. Run the web server as mptsuser. If you can't change this webserver, maybe you can install another apache for yourself on a different port.
  or
2. Write a perl script that is run as mptsuser by cron once a minute. Change your cgi script so that it creates a file telling the cron script what to do. If the one minute delay is bad, put a loop in your cron script so that it sleeps for a few seconds and checks for the file, repeating until just under a minute has passed.