Dear Kevin,
This discussion also arose when we announced the deprecation the first time around. I think David started to work on a REST api for Ontopia around that time, which is still in the sandbox. I don’t know the status of this project, you would have to ask David. What we at Morpheus have done is create our own REST API (actually way before David began his work) which, in the core of it all, relies on Ontopia interface methods and TopicMapBuilderIF implementations to do topicmap modifications.
For quick-and-dirty work, one could also use these methods in a JSP file that handles form posts. This also allows you to model your own business constraints.
So we don’t really have a full replacements yet. Maybe after this migration drama has passed we can set out a plan toward Ontopia 6.0.