I use something similar, although I bundle it all into an 'upgrade.php' script which contains all the sql changes and updates the meta_data like table for you; as the 'admin' you just need to hit 'upgrade.php' every once in a while and off it goes.

As an example, see http://postfixadmin.svn.sourceforge.net/viewvc/postfixadmin/trunk/upgrade.php?revision=794&view=markup

the only downside to my approach is that it doesn't (yet) support reverting to an old configuration - something I've never found to be necessary so far.

I think the postfixadmin one takes into account the svn revision number; while on other projects I just use a sequential number.