Working with freetagging autocomplete fields

Assuming not, my current inkling would be to see how to use the Chosen liszt:updated event to update the field, hooking that into the taxonomy module.

From the documentation
http://harvesthq.github.com/chosen/

Updating Chosen Dynamically
If you need to update the options in your select field and want Chosen to pick up the changes, you'll need to trigger the "liszt:updated" event on the field. Chosen will re-build itself based on the updated content.

jQuery Version: $("#form_field").trigger("liszt:updated");

But that would only get us half way, the taxonomy_autocomplete would also need to be hooked into to pass the user's input.