Hi there, Janwswan!
As you say, you're a Believer, and THAT, friend IS your answer. As others here have said, you will find as many different pieces of advice and experiences and reasons to stay or go, as there are people! Actually you'll find double.. because there's always the "what if's": what if we had stayed? What if we went? What if we don't like it? What if we can't afford to come back? Or, I wish...
The answer as a Believer, is not to look at the circumstances or the What-if's. It is to ask Father God what His will is for you and your family. The fact that you have been approved in principle (as I understand?), is quite a big thing. For many this is a far more difficult process, but as your wife works in the medical arena, she is sought after in any country, and therefore you've had the privilege of coming through relatively easy (or at least so it seems from what you've told us).
I would like to make the following suggestion.
And this is a suggestion only! 
Go through with getting the PR in your passports when the time comes. When Babes arrives, enjoy him/her and make sure the Grandies get to see Babes and enjoy him/her. Wait a few months for Babes to grow a little, and then come over to NZ to take up the residency (around Nov - before Dec peak times!). At least then you have it in your passports that you ARE residents. Come and check out the place, if you can afford to, for a few months. Make contacts, take a look at the job market and the options. Get a feel for it. Perhaps by then you'll have peace in your hearts anyway for whether it's God's idea to move here or not. You can still return to live in SA. I'm not sure what the requirements are to retain residency, you'll have to read that up, but you can live a large portion in South Africa, and still retain it. At least give yourself that option.
The choice for whether it's best for your children to raise them in SA or in NZ, is a really hard one. Let's weigh up the pro's and con's and you can add some...
PRO's for moving to another country (NZ or wherever)Your children get to grow up without the ongoing fear of being mugged around every corner. (not that this is necessarily true of all areas of SA either!).
They get to riding bikes in the neighbourhood and opening room windows that don't have burglar bars on, not living in jailed home.
They get to going to university where the degree is more readily recognized than SA ones (not that this seems to be a major problem right now, but the education system is going downhill there too, and it seems that more and more, countries are wary of SA degrees being on a par with theirs).
They get to growing up with diverse nationalities and not necessarily looking at other skin colours as something to be feared, but something that is part of the diversity of God's creation.
They generally grow up with a broader worldview than most kids whose parents have never moved further away from their home town than a few hundred km's.
As for work for you:
In the medical field your wife will always be on the "wanted" list.
In the agricultural/science field, you will also be sought after, esp here in NZ, where there is still a very live agricultural culture. (Esp here in the Waikato where we live!
)
Where pensions are concerned, depends on how young you are. As far as I can see, personally, no country has a very secure "pension" scheme, and it is always a wise move to invest in your own Retirement Annuity and not depend on government. (that is my personal opinion and may differ from others!)
There is a lot that NZ has to offer in outdoors recreation that is free and mostly without fear from "predators".
That said, NZ is not perfect, as is the case with any country in this world that you may choose to look at.
The CON's:You move to a new country, where you have to build new friendships from scratch, and it takes a lot more effort than it did back home.
Your marriage WILL be tested. The foundations of your marriage will be shaken, so be sure they were built on the Rock!
Your kids get to grow up without the family close by - you have to hire sitters when you want to go out, you can't just dump the kids on Grandma or Sis.
You move to a country where the government is wanting to govern how you raise your kids in the home (but I've heard this is happening in SA too anyways). The thing to remember is, stick to what you know is true, and trust God to sort out the rest. (BTW, He gives you new friends and family too!
)
PRO's for staying in SA.Your kids get to growing up close to their grandparents, and perhaps even cousins.
You have friends around you that have been part of your culture and history and when you get together you enjoy a shared history and understand each other's jokes. (but that can be found here in NZ too, there's enough of a Saffer invasion here!
)
If you know that staying is what God wants you to do, your kids will grow up knowing God's protection.
What if the "popo hits the fan" in SA and we did not go, what am I going to tell my child?
You'll tell your child the truth - that you made the decision you thought was best at the time.
And that will also be the answer, if you do decide to move, and your kid asks years down the line, but why did you leave SA, where our grandparents are? Why couldn't we grow up around family? Same answer, because that is what we felt was the best decision.
It will be a lot easier to answer those questions, if you and your wife sit down together and pray, and wait on God's guidance. Then when the kids start asking those questions, you can answer them with confidence, "We did what we did, because we were being obedient to God's calling."
I've done this whole thing twice. Once without children, as an exciting adventure with my husband; with the idea that if we didn't like it we could come back. 9 years later, we did it again, this time with 2 children. Let me tell you, moving countries with kids is not easy, esp if they are too young to understand why we need to move. And having to not only cope with making friends for yourself and making inroads into the new culture for yourself, but helping your children through the process too. It's a hard road to walk. I'd say we've had our fair share of "sakke sout saam opvreet"!
All the best Janwswan! At least you have time on your hands to make this decision!
(sjoe... didn't mean to make such a lengthy post, but hope it helps somehow!)
