@MarcoAurelio, when we did that (rename namespace) for the Walloon Wiktionary all we needed to do was change config and then run namespaceDupes. However, since cawikimedia doesn't have any pages in the "Project" namespace or any pages in the main namespace with the prefix "Wikimedia:", I'm not even sure you'd have to run that script. Should still do it just to be safe though.
Ohh, sorry, I've missed one line, thanks.
I've created a patch for this change, by just removing the line that define the namespace exception. Will deploy this in swat in next days with the other.