But they did not rename any existing repositories (that would be in very bad taste!). Such an automatic renaming would possibly break a lot of scripts, but this is not what is happening. All old repositories still have their branch names intact. The new repositories can have whatever name you choose.

What does "the change" actually do? Is it just in the "new repository" instructions or is there some automated process that may fail? Maybe I'm missing a way to create github repositories besides the "New" button on your user page?