[eluser]Valdemar[/eluser]
That's really a bad way to have php installed :-) I'm unsure why your university would keep it like that .. you can still use php in cgi mode without forcing the file extension and having to add the php binary executable (what was the name .. shebang?) in the first line.
There might be a simple solution to your problem if you have the permissions (and also if you are using Apache) to override the apache php handler. In short, you will need to edit your .htaccess and add something like:
AddHandler application/x-httpd-php .php .php3 .php4 .php5 .phtml
This will instruct Apache to parse any file with .php/.php3/.php4/.php5 or .phtml as a php script.