When registering a taxonomy if you set the ‘meta_box_cb’ argument to false then the WP box for the taxonomy will not appear.
I don’t know about the feature to prevent ACF from saving the values as normal. The best way to get feature requests looked at by the developer is to create a new support ticket: https://support.advancedcustomfields.com/new-ticket/
It is possible to abort the saving of data to the field in WP using this: https://codex.wordpress.org/Plugin_API/Filter_Reference/update_(meta_type)_metadata
