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There is a method in *nix/Apache to run the server with a suexec so that the server is running as the user of the website.
This also has the effect of limiting the scope of your scripts to effecting only those files which the user has write access to. Thus you don't have the problem of any user with group "nobody" effecting files written by another user also under the group "nobody".
This does mean you are still subject to the problem mentioned above of any files written by the website user will be at the mercy of scripts running from the website.
As an aside, I like the looks of cgiwrap mentioned above.
If you are concerned about other idiots on the same box as yours causing damage, one solution is to get a colocated server thus removing the other idiots on the box and narrowing the scope of idiots to just one. ;-)
If the project is worth the $300 to $500 per month of most colocated servers this might be an option.
Hope this helps
p.s. A word to wise when creating script which directly modify files on your website HTTP_REFERER is not a trusted field. Paranoia is your friend. Taint is a must.