It's your choice, as always, but the general opinion on matters like this tend to be along the lines of:
Don't make your CGI programs run as anything but a non-'sensitive' user.
If you do need to get your CGI programs to do super/normal user style activites, try and make it so that a second set of programs (outside of the Web Servers Document path) actually do the dirty work.
The second set of of programs can be set up to run at the correct security level.
That way your Perl programs can remain 'un-enpowered' and the programs that need to do the more sensitive work are kept safely out of harms way.
I realise this hasn't actually told you how to do anything, but it's something best learnt the 'easy way'.
Regards,
Luke