Not quite following, but IF both are current, valid passports, then as long as the ticket is in the name of the passport being used, should be OK.
Therein lies the problem as the air ticket can only be in the same name as one of the passports.
From an airline perspective, when your wife checks in at BNE or AKL Airport, airline staff need to see the passport you will be using to enteri the country of your final destination which in your wife's case is Crimea so if her Ukrainian passport is in her maiden name then the air ticket would need to match that.
From a Customs perspective, when she departs BNE or AKL she must use her NZ Passport so you will need to find out from Australian or NZ Customs if they have an issue with the NZ passport (in her married name) not matching the name on the boarding pass (maiden name).
The reverse situation applies on the return sector as checkin at SIP Crimea would be wanting to see the passport you are entering BNE or AKL on which would be the NZ one, so they would want the airline booking to be in her married name.
Again there could be an issue with Crimean Customs if someone's boarding pass in married name does not match maiden name of Ukrainian passport.
I suppose it's not possible to get a Crimean (or soon to be Russian) visa in the NZ Passport and just travel on that one when your wife is still a citizen of that country?
One way around it would be to book two one way tickets provided it wasn't a lot more expensive than a return ticket & book the BNE or AKL to SIP outbound ticket in her maiden name then the SIP to BNE or AKL inbound ticket in her married name. This scenario would still need Customs of both Aust or NZ & Crimea to be okay will departing that country on a passport that does not match the name on the boarding pass.