A very secure option is to put the PHP parser binary somewhere outside of the web tree of files. In /usr/local/bin, for example. The only real downside to this option is that you will now have to put a line similar to:
#!/usr/local/bin/php
as the first line of any file containing PHP tags. You will also need to make the file executable. That is, treat it exactly as you would treat any other CGI script written in Perl or sh or any other common scripting language which uses the #! shell-escape mechanism for launching itself.
To get PHP to handle PATH_INFO and PATH_TRANSLATED information correctly with this setup, the PHP parser should be compiled with the --enable-discard-path configure option.