There is no departure/arrival segregation or rescreening at the domestic terminal. It's a fairly crap layout to do this, even with temporary hoardings.
There's also no biosecurity or customs / immigration facilities.
To go to the cook islands you are leaving/entering New Zealand territory so there are very different requirements.
Agreed there are requirements but I am sure that appropriate faculties and processes can be stood up to differentiate bubble connecting flights (wherever they are to and from) and non bubble international flights. It is a problem that requires and must be solved.