The NZRU financial independence is whether they like it or not, linked to the Australian game far more than linked to the South African game, the fact is tho that the NZRU see benefit from a rugby perspective through South Africa.
Unions are propped up by TV dollars more than anything, cannibalizing the Australian market would mean less content at time slots that can be sold off to advertising agencies for peak dollars. Therefore a smaller pie would be offered from Sky. Not having Australia in Super Rugby would be a massive win for the NRL as they would dominate television audiences (in NZ) purely on the fact they offer a product at a time accessible to everyone.
The NPC is also proof that the game in NZ is not financially viable on its own, just like any competition here by ourselves isn't viable on our own. Its a great rugby nursery but it isn't even near the ball park to retain any level of elite professionalism in NZ.
I'm going to deal my hand out there and predict that in 10 years time an Aus/NZ competition will happen, either in the form of a domestic conference in a reformulated Super Rugby (not the shitty one delt with now) or an independent Trans-Tasman competition. The power brokers at Sky and Fox would kill for a greater control over content, fixtures, times, to maximise their investment. The money they could generate through being able to place games on Sunday's, Monday nights, ANZAC day clashes would be a game changer for them both. But because NZRU is rightfully looking after their brand which is reliant on being world renowned as the 'worlds best', they are capitalising on this like any business does, a dollar today is worth more than a dollar tomorrow. However with the improvement of teams up north and their growing financial muscle the tide will turn where they will have to offer something other than being the 'worlds best' because that wont be forever, the increased globalisation of rugby will see the days of teams being unbeatable against others over, similar to football just on a smaller scale.