I think the difference is that Mauna Kea is uniquely suited for an observatory and happens to also be sacred. I’m not surprised a place with such clear views of the stars is sacred. Mt. Rushmore is different. There’s nothing that makes the Black Hills uniquely suited for a tacky sculpture. It was constructed out of spite and the site was chosen to prove a point.
You're not wrong re:Rushmore, but I think you overly privilege the perspective of the scientists who are displacing the native Hawaiians. From the native perspective, there's less difference between "monument to the greatness of the white colonizer" and "huge set of instruments that are used almost exclusively by transients that don't really contribute to the native community". The problem isn't the intent of the builders (there's a decent argument that spite and dominance were not on the agenda for Rushmore), it's that that nobody considered the people being displaced.
Also, Mauna Kea is arguably unique in US territory for seeing conditions, but it's by no means unique in the world. A lot of the same people I worked with who had collected data at Mauna Kea also did so at Cerro Tololo and other telescopes in the Atacama desert. But it's definitely unique to the Hawaiians. In that sense, it and Rushmore are very similar.