We have a custom master page that is deployed to the MySite web application per these instructions - http://www.sharepointblog.com/2008/07/sp2007-custom-master-pages-on-subsites.html
However, we require the ability to deactivate the feature on all the site collections that are within the MySite webapplication. The feature is built as a site collection scope. How would we deactivate them on an application that has potentially 3000+ MySites?