But you can also understand Smith's point of view. Ipswich Town, despite several close shaves, haven't been in the Premier League since 2002, and have the longest current tenure of any club in the Championship.
In his seventh season with the Tractor Boys (he is the longest-serving player at Portman Road), they sit two points outside the play-off places. Every point is vital, in probably the hardest league to earn promotion from in the world. Ipswich host Birmingham four days before the Tokyo match and visit Middlesbrough three days after it.
The All Whites' next major goal is the 2016 Oceania Nations Cup, so if a game is going to be missed, now is the time.
But just as Smith needs to be wary, New Zealand Football need to tread carefully with Smith. Whatever happened in his head before the Mexico play-off (like many of the senior players in the side he was thoroughly frustrated with what he felt was substandard preparation in the preceding months), he performed well in hugely difficult circumstances at the Azteca Stadium and in Wellington.
He is a capable captain, and spoke with passion and admirable frankness after both heavy defeats against Mexico.
Smith has proved his pedigree on the global stage - particularly at the 2010 World Cup - and the New Zealand side is not blessed with experience in that area (four of the five defenders in the squad to play Japan have just 16 international matches between them). The youngest captain in All Whites history, he is still only 23 and has already accumulated 22 caps.
Smith's absence against Japan gives Andrew Durante a chance to impress at international level after disappointing performances against El Tri and offers Ben Sigmund a lifeline after he fell out of favour last year.
Meanwhile, the All Whites look in good heart despite the turmoil of the past year. One-third of the 18-man squad are based at European clubs and all but two are with professional teams.
There is also hope around the young guns, including Marco Rojas, Bill Tuiloma, Ryan Thomas, Storm Roux and Chris Wood.