I do remember that someone posted on the forum that the CO had raised the issue of their having different religions.
However, I've never heard of the fact of ONE family member's, even a parent's, attitude making a big difference, and your CO didn't, from what you say, pick up on the mention of your father's feelings.
Also, there is no basis in the requirements for partnerships visas for anyone to follow all or any tenets of their family's religious background.
https://www.immigration.govt.nz/new-...-visa#criteria https://www.immigration.govt.nz/new-...ly/partnership
As EGoodhue has said, it would be very surprising if this CO raised any issues on this matter. If he did, you have strong arguments that this is not justified by the requirements.
The rest of this is my thoughts, nothing official.
I would add that there must be a high proportion of families, with no difference in background or religion, where at least one of the in-laws is never happy about their child's choice, and that included my own m-i-l, despite my solid marriage going on before her eyes for 40+ years.
NZ law does not support parents (whatever their cultural or national background) having a veto even over the choice of marriage partner of their adult, non-dependent child.
https://www.govt.nz/browse/family-an...who-can-get-it
You can’t legally marry if you’re:
already married or in a civil union, unless you’re changing your relationship with the same person
closely related by birth, marriage or adoption
under 16.
Full list of people you can’t marry — Marriage Act 1955
There's no requirement there for religious agreement or parental consent. That being the case, there is even less grounds for anyone looking for all-round approval about who their adult children decide to associate with, then set up home with.