I would have thought that by confining the passengers to the gate or at least the "Secured Area" (Can't quite remember the terminology for an area in an airport that comes after customs and security) that therefore they would not have to be involved?
US airports do not have outbound immigration/customs. The US has no regulations that require it, and hence all outbound international flights operate from normal terminals with the exact same security setup as any domestic flight. Immigration and customs only applies to arrivals.
(This is one reason you can't transit the US between two other international destinations, for example Australia to Canada, without entering US immigration - there's no "secure" transit area where you can remain separated from the normal domestic terminal.)
As far as the JQ flight not returning to the gate earlier, I suspect it's much more about gate and staff availability, and the potential to lose passengers who wander off. Although I seem to remember HNL's "overseas terminal" being deserted in the morning when QF and JQ arrive and depart, as most flights are to the mainland US and depart in the evening, so it seems unlikely gate availability would be a problem.
The US has a "passenger bill of rights" that issues steep fines for US airlines remaining on the "tarmac" for more than 3 hours. In accordance with this, airports are now set up to ensure that a gate, or at least a parking area with buses, is available for flights after 2-2.5 hours of delays. Although the JQ flight wouldn't have been subject to this rule, the delay is considered acceptable by US standards so I don't think the passengers really have much to complain about.