Not really an answer since I don't use mcrypt() myself, but a third alternative could be to just install/enable mcrypt() over the current PHP install:
I personally always do use existing PHP, the version FileMaker installs is typically pretty out of date from a security standpoint compared to the latest you can install yourself.
Have you got this working yet? I have just gone though the process which Mike pointed out on Aug 3. I cannot say it was entirely hassle-free but I got there.
It is essential to locate the Filemaker Server instance of php.ini. Before you start make a phpinfo.php page so you can look there for the file indicated by 'Loaded Configuration File'. At the end of php.ini you need to enter BOTH load instruction for mcrypt AND the pointer to its location as per the instruction at the end of the Coolest Guide page. They do live up to their name.
Next thing for me: installation of simpleSAMLphp. Slightly harder as you are on your own in tweaking its config.php and _included.php files to match the non-standard location of the FMS php installation once again. I ended up putting the entire www folder of simpleSAMLphp at the webserver docs root level and changing the file pointers inside the _included.php file to the server machine's home folder where the rest of simpleSAMLphp resides. The documentation says to use /home/[username]/... but it should be Users/[username]/... Still not entirely up and running but I should get there with some perseverance - and the help of others.