It sounds like Public Folder support will be around for quite a while due to how often they are used for versions of Exchange before 12 and especially Outlook clients before Office 2007. You will be able to disable Public Folders in Exchange 12 but you'll lose a lot of features.
I think this is a step in the right direction, honestly. Public Folders have always been a bear to maintain when they get into the multiple gig range. You could think of the backend of Sharepoint 2001 as one big public folder, because, that is essentially what Sharepoint 2001. It was a custom version of Exchange 2000 backend with one information store. I still have nightmares of maintaining a few huge SPS 2001 sites. It loved to eat folders for breakfast and require a good ISINTEG every year or so to clean up the cruft.
WSS v3 will be the platform to build 'new' Public Folders off of, and I think that will be pretty cool.
More info here:
http://blogs.technet.com/exchange/archive/2006/02/20/419994.aspx