Right now, you currently can't mix users on the same mailstore; while you can turn individual services on and off for individual users/only distribute connectors to certain individuals, the problem becomes enforcing it.
Some of the things easily turned on/off: Address Book, Calendar, Documents, Tagging, Sharing, Change password, Change UI themes, Advanced search, Saved searches, Initial search preference, IMAP access, POP3 access, External POP3 access, Allow the user to specify a forwarding address, Conversations, Mail Filters, HTML compose, Out of office reply, New mail notification, Mail Identities, Zimbra Mobile, GAL access, Autocomplete from GAL, etc...
I would suggest talking to sales AT zimbra .com, they may be able to strike a deal with your issue.
I know there's been other's with this thought in the past-I have myself
Other threads on this issue:
Also search bugzilla, there may be an RFE for 'mixed NE & OS licensing'.
While it wouldn't keep anyone from distributing the NE connectors, it would apply some of the following things to only NE users: backups, attachment indexing, zimbra mobile, HSM, etc. Clustering support would be tricky though, it would still require forcing users to separate NE vs OS mailservers...