I would probably handle this by showing an error message “notification” that the my plugin requires ACF Pro which is included with the plugin and ask them to deactivate the free version of ACF. I might also provide a link to allow the to deactivate the plugin in the notification. If I did this I would also build in some type of detection on my admin pages to reduce the functionality because some field types are missing.
Alternately, if you want to be more forceful you could automatically deactivate the free version when your plugin is activated and then if your plugin is deactivated and the free version of ACF is available to activate it again.
