We have the same situation here with a lot of native tribes. Let’s take the Navajo for example here in Arizona. If the state govt were to build a quarantine facility outside the control of the Navajo and send Navajo there for all the same reasons you stated, there would be the same outrage by pretty much all sides. Quarantine camps are not acceptable here though they might be in Australia.
The thing is, this facility was not built to house indigenous people. It was actually set up to deal with illegal immigrants - boat people. Australia doesn’t currently have that problem in any significant way but there have been periods in the recent past when thousands were arriving every year, and because the Northern Territory is about the closest point of Australia to South East Asia, they got the brunt of the arrivals.
Because it’s there, it’s being used. In other parts of Australia, when people are quarantined - and they sometimes are - it’s generally in hotels. And that hasn’t always worked well (99% of Victoria’s second wave was directly linked to two breaches of hotel quarantine).