We've got a couple of mirrored Linux machines acting as servers for an ISP. (I must warn you: I am very much a Linux newbie.) I have gotten used to setting up regular new users, who just need to be able to access their web space, but now I have to deal with something new -- to me, that is.
We have our main website on an NT server. We have a company putting in some CGI scripts for the site. The person writing the CGI scripts is comfortable with Linux, but not with NT. I, too, have had trouble getting CGI scripts to work on an NT machine, and I have been putting the scripts on our Linux machines, and just pointing the forms to the cgi-bin on the Linux machines.
I have never tried to give anyone else permission to access the cgi-bin. I have created a user account, and put it in a group.