Starting from version 1.12.0, the free Tag Groups (Base) plugin is already bundled with Tag Groups Premium. That means that you need only Tag Groups Premium. If you also have the free plugin, it is automatically deactivated.
If the free Tag Groups plugin is automatically deactivated, there is no problem to remove it. Just make sure that in the Settings you have not previously activated under the "Reset" tab the deletion of the settings and tag group data.