Should I keep things the way they are, label PDF::OCR as deprecated ...

Yes. You went through some trouble (and took some undeserved crap) to avoid breaking other peoples code. ++

Going back now and breaking that code, for no reason other than some people do not like the PDF::OCR2 namespace, is not the right thing. Also, what about the people using PDF::OCR2? Will they now need to "upgrade" to PDF::OCR?

IMHO, its easier and less troublesome for everyone involved if you just continue on the path you started. Just update the docs to state that PDF::OCR is depreciated and no longer maintained, and PDF::OCR2 should be used for new projects.