I too experience the reappearing 'deleted' history.
The probable explanation is that iCloud still stores the map data.
So you would need to turn off iCloud Maps to prevent iCloud from synchronizing map data. Go to Settings-> [username]Apple ID -> iCloud -> Turn off Maps
To clear all of your history from your phone...
Go to Settings > Privacy > Location Services > System Services (scroll to the bottom)> Significant Locations. It will need your touch ID to view Significant Locations.
From there you could either scroll to the bottom and clear all history (including any favorites), or you can select one of the locations shown, slide to the left and tap delete... to delete just that location.