We were able to use another WordPress plugin to force WP to send confirmation emails with verification links before the users account becomes active.
The plugin we are using is called Ultimate Member; the free version includes this functionality. One thing to be aware of is that it has it’s own login/member page system. We have been able to integrate it pretty seamlessly with GeoDirectory, but our use case may be a bit different than yours.
If this plugin doesn’t work for you I would assume it would be pretty easy to find another plugin which suited your needs without having to modify GeoDirectory.