Is the league that fragile that another team playing in Auckland in a different competition will ruin it? I imagine it'd still exist as it does now, and the playing level may even increase as more see an opportunity to showcase themselves for a gig at a professional club, of which there would now be 2 in nz, one of which is centred in a massive population base - it may even help create the need for a third Auckland team in the ASBP.
There is my case to say it would be positive for the league. You're yet to detail how exactly it would bring the whole league down (across the entire country) if there were an A league side in Auckland. Especially since the Phoenix did nothing of the sort - and in fact the nix did a lot of the positive things that I mentioned above to an extent and that would only be an even greater effect in Auckland.