It depends a lot on one’s character, but I’d consider that after living for 4 years in a city with your family you might not be so inclined to move abroad and start again from scratch.
And depending on what she’s studying it might be easier for your wife to find a job in Switzerland if she studies here.
I think that even if in the short term Munich is close, in the long term Zurich becomes a no-brainer. The higher income (once you start earning 2 Swiss salaries) should easily compensate for the relatively short-term childcare costs.