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Joubert sin-binned All Blacks prop Owen Franks and Wallabies wing Drew Mitchell for seemingly innocuous tackles in the first half, then red-carded Mitchell two minutes after the break for deliberately holding up play.
"I think it's good they're strict. Okay, there might be some debate about some of the decisions, there's always going to be some debate about the decisions," Henry told reporters on Sunday.
"What you don't want is referees being soft and therefore you get a game that doesn't flow and there's a lot of illegal stuff happening at the tackle.
"If he's grey at the tackle area or he's grey on people throwing the ball away when the other side wants it, you've got a shambles on your hands.
"So I think it's good that he's strict and he sticks to what he says he's going to do."
Henry said his team had played "exceptionally" well in the crushing win that delivered the All Blacks their eighth successive victory over their trans-Tasman rivals and propelled them 11 points clear of Australia on the Tri-Nations table.
"There were some dull patches and some mistakes and we'd like to eradicate those if possible but you have to be pleased with seven tries," said Henry, whose team notched a bonus point before halftime.
The All Blacks head to Christchurch this week for their next Tri-Nations match, against the Wallabies, with only one fitness concern clouding scrumhalf Jimmy Cowan, who came off the ground early with a rib cartilage injury.
"Apart from that I think we're pretty good," Henry said.
"I think it'd be a miracle if (Cowan) played next week. He'll probably be right for South Africa (on August 21)."
Cowan's injury could open the door for Blues scrumhalf Alby Mathewson to be recalled to the squad for the Christchurch match, where New Zealand could possibly seal their fifth Tri-Nations title in six years.
