The accepted solution thus far has been to install newer versions of PHP alongside Apple’s version using Homebrew or MacPorts. This would likely require you to compile the MCrypt extension manually. I also found that Homebrew could leave your system in disarray if things went wrong (more than once I had to do a complete restore because of this).

However, there’s another method I came across while research some non-related issues: install the latest version of PHP from a binary that includes the MCrypt extension. It will not bork up your system if you want to remove it, either.