You will need the Check-In permission to perform this action.
Click on "More > Check-In > Stations" in the left hand navigation. Then select "Delete" from the drop down menu at the end of the row containing the station you want to delete. A confirmation message will appear. Click on "Yes" to finish.
The station will immediately no longer be authorized to perform any actions in the check-in system. Even if it was in the middle of a check-in.