Your Home directory is at the center of your installation's filesystem and, therefore, Mac OS X prevents any potentially malicious application from moving it or tempering with it.
However, there are ways to backup a whole Home folder quite easily.
May I suggest, for example, that you have a look at applications like this one ?
Would you like to write your own script, you may want to use a shell script ( i.e. UNIX commands ). Indeed, since these scripts can be easily given additional privileges for a limited period of time, they will better interact with Mac OS X when it comes to working with essential system files.
Would you be an experienced AppleScripter, keep in mind that shell script commands can be included in an AppleScript.
Let me know if this helps !