place the functions.php file outside of the apache web root. this way the only way the file can be included is by the local server referencing the file system path to the functions.php file.
for example if the apache web root is:
/home/httpd/html/
then place the functions.php include file:
/home/httpd/functions.php
now apache won't be able to sent the file out. have your php scripts load the functions.php file like so:
include("/home/httpd/functions.php");