The latter, since it works both where you have root and where you don't. This way, if you ever have to re-host your site elsewhere, you won't need to revise every single CGI script.

In general, the traditional practice of "avoid using root whenever you can" is a good one to follow; root access is for handling situations that can't be managed any other way. As root, you can always fix the problems created by non-root users - but the reverse is definitely not true.