Hadden made 13 changes from the side which defeated Romania on Tuesday, leaving out most of his key players in order to keep them fresh for the crucial quarter-final decider with Italy in St Etienne on Saturday.
His scratch side, including new caps John Barclay and Alasdair Dickinson, frustrated the All Blacks for an hour before New Zealand crossed for three tries in 20 minutes - but as an exercise in damage limitation it was reasonably successful as their opponents claimed a 40-0 victory.
Scotland now leave Edinburgh to return to France still searching for their first win against New Zealand in 102 years and in the knowledge that their pivotal match in the tournament is just six days away.
Hadden said: "It's not our decision to have the World Cup format the way it is. When I looked at our draw for the first time and studied it I couldn't believe it.
"Having accepted there was nothing I could do about it we obviously decided to crack on with it and do whatever we needed to do to go as far as we possibly can in this competition. I'm not unhappy with where we are at this moment.
"We are delighted we have a team that can actually practise tomorrow and that is a huge bonus.
"We haven't selected the team for the Italy game yet but having so many guys available to us because the medics have done such a good job is tremendous and we're delighted with that."
Hadden also denied the decision was in any way a gamble and praised the performance of his debutants in the pack.
The former Edinburgh coach, who revealed that Chris Paterson was forced off with an eye injury but that it was not serious, said: "We are not going to be judged about how successful we are in this competition this week.
"Personally I never thought it was a gamble. I thought it was an excellent opportunity for a lot of guys who haven't played too much this season to put their hand up for selection at this stage in the competition and they will definitely feel that in the days and hopefully weeks to come."