It might be a rare case but since the denying author has major contribution, would in such case the paper be never published or there are any other way(s) that would otherwise not breach the ethics of publication.
Why does the denying author not want the paper published? It will be important to explore the reasons. Is it perhaps that it requires further work or is a question about quality or impact? In other words, it could be that there are valid reasons for not wanting to publish....
Also, was the intention to publish made explicit by all authors upfront, during the ethical clearance process and prior to the research being conducted? If this is so, and there are no valid reasons for not wanting to publish, then "pulling out" later in the process could be questioned.
Check with your Ethics Office or Research Department. Or consult the relevant research ethics policies at your institution.
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