Ignoring which category country you are coming from, the rule is any one below 12 years old or any kid that has not been vaccinated will need to quarantine 21 days. Therefore they need to be staying with a parent be it wife or husband because no hotel will allow a minor to stay alone (some hotel allow a certain teenager age to be alone, I think 16 above)
You never mention what visa status is your wife, if they are not holding a resident visa, ie they are coming as tourist and applying visa when in HK, then your HR is right, she cannot board the flight because only HK resident from high risk countries are allowed in. Non-resident can only come from medium risk countries provided they are fully vaccinated