The article actually addresses some of the cases you mentioned - like families and couples - and proposes exceptions for those. You could conceivably implement

The article actually addresses some of the cases you mentioned - like families and couples - and proposes exceptions for those. You could conceivably implement a check-in time boarding order assignment algorithm which takes such factors into consideration. This would result in a slightly longer than ideal boarding time, due to congestion in the aisles, but still better than the current scenarios.