It appears that the haka wasn't expected at this event. If it's common at NZ universities, do they have protocols in place for it?
My main etiquette issue is that, in general terms (ignoring cultural issues here for a moment), it's rude to hijack one ceremony (the graduation) for a ceremony of your own. However, perhaps this is already included in the protocol for a NZ graduation, and isn't "hijacking", but part of the standard.
Perhaps I'm jaded, because I've grown used to graduations where the families are not even allowed to clap for their graduates, because it slows things down too much. If certain families were allowed leeway to have exuberant celebrations, I can see a lot of other families going, "the heck with this, I'm going to take time to celebrate MY kid as well", and the whole thing bogging down into a chaotic mess. If this isn't a problem in NZ, and other graduates are not drowned out by the haka, then it shouldn't be an etiquette issue.
I hope that clarifies my position somewhat?