We resolved the issue and dropped CPU usage in our script dramatically last night and informed GoDaddy.com immediately, however the database remains offline 12 hours later (They must have slept in today).
In the email:
Unfortunately, we are not able to troubleshoot custom scripting, and therefore, we are not able to provide specific solutions. Once you have identified the cause of the issue, please reply directly to this email with the steps taken to resolve the issue.
Well, essentially eliminating the ability to create large page listings is the only functionality that can be removed and has been. Statistical information has been removed as well to lower CPU usage further.
If I remove anything else, users cannot view the site . Here are the steps that should be taken: "Fire the person in charge of the CPU usage problem, hire a real linux tech, get them to implement CPU throttling" and voila... no more reason to damage sites at will, no more cross-site CPU hogs.
Needless to say, we will be looking at other service solutions that will not prohibit access to information (Is the owner a communist?)