INZ isn't being unfair, in itself. The politicians sign off on the laws governing the granting of visas, and INZ have to apply the regulations as written.
SM1.5 h: If an offer of ongoing skilled employment (see SM6) is obtained during the deferral period, the application may be approved.
https://www.immigration.govt.nz/opsmanual/#66762.htm And see SM6.30.10.
https://www.immigration.govt.nz/opsmanual/#66791.htm For residence to be granted to the JSV holder, s/he has to have, at the time, a skilled job which, according to the contract, will go on into the future (for at least 12 months, and even then, the employer has to show good reason why it's only that long).
As EGoodhue says, one would hope that time will be allowed for the employee to find another skilled job. INZ do have a past record of giving some time for fresh job hunting in the slightly similar situation where someone's residence under SMC application is being processed but then they are made redundant from their skilled job.But however sympathetic the official may be to the individual applicant, ALL they can do is delay closing down the processing because the conditions are no longer met, to give the person a chance for another job, and I'm sure the line-managers wouldn't be allowed to turn a blind eye to things being stalled for TOO long.