I came across this issue the other day. When creating a custom master page, I then wanted to delete it. When trying to delete the page I got the following error
"This item cannot be deleted because it is still referenced by other pages. This item cannot be deleted because it is still referenced by other pages "
but I knew my page was not attached to any other pages. I finally found this KB from Microsoft http://support.microsoft.com/?kbid=926812 stating this is a known issue.
Rather than "hiding" the page as they suggest, I chose to create a Folder called "DeleteMe" in the MasterPage Gallery, then I had to turn my Version Control off completely and Content Approval off too. Then I opened the gallery using SPD and was able to drag the master pages into the DeleteMe Folder, then I went back to the Master Gallery web page and deleted the Folder