If you really managed to not only delete
/usr/bin/php (which could be easily restored from a backup or another Mac), then your only easy option is to reinstall OS X. Doing so, it will leave your user files in place (i.e. the one in
/Users) but it will overwrite all system components, including the packaged versions of PHP. Upgrading OS X is also possible in this case – it will have the same effect.
You can reinstall OS X Lion or Mountain Lion by booting into Recovery. Just hold CmdR while startup and reinstall OS X. Make sure you take a backup of your entire system before though.
In the future, if you want to work with other PHP versions, consider using MAMP, a standalone package that comes bundled with various PHP versions to choose from (including 5.3 and 5.4), which does not interfere with your system binaries and frameworks.