Only thing that comes to mind is a wrapper script for /sbin/shutdown which checks if root is logged in on console or via pts/[0-9]. Other than that I don't see how you could disable it for root just b/c that user is logged in remotely.
Why not just have the person logging in remotely use a regular account and give him "sudo" access to only certain commands. That way he/she has root access to certain things but not everything. Please google "sudo" if you're not familiar with it. Fedora has it installed by default as far as I remember. If not do a "yum install sudo" without quotes from a terminal window.
By the way, /sbin/shutdown is a binary so you can't open it with an editor. You could run a "strace /sbin/shutdown" and see what system calls it makes. IE: which files it opens which you could then place the appropriate "remote login" check in there. I believe it goes through the list in /etc/rc5.d/K**somescriptname where ** is a two digit number. My first shutdown script in there is "K01smolt". You could place a little code at the top of your first shutdown script to run this check, if logged in remotely, kill the shutdown process. Would be tricky