The Constitution prevents the Federal government from interfering with freedom of association, as it does with the rights of free speech and religion. Those rights are neither defined nor guaranteed by the Constitution, they are considered to be inalienable rights endowed to all peoples by God.

Private entities are allowed to choose with whom they associate, or not, barring protected groups defined in Federal law. This is why businesses have a sign on the door that says they have the right to refuse service to anyone. Rights not permitted to the Federal government devolve to the states, and then to the people.

Also, it's Hawaii. The native government was overthrown by a coup orchestrated by American sugar companies. It is one of many sovereign indigenous nations being unjustly occupied by the US. The Constitution is on their side but I hold them to no obligation to give a single rat fuck about colonizers and their laws.

Constitutional guarantees are in "tension" with each other. (That's the phrase I've heard lawyer-type people use.)

The Constitution also says that Congress can regulate interstate commerce, Article I, Section 8, Clause 3. Eg, in Heart of Atlanta Motel v. United States, the Court decided that the motel's racial discrimination hinders interstate travel, and thus under the Commerce Clause was required to follow Title II of the Civil Rights Act of 1964, despite the motel's owner arguing (among others) "that it violated his Fifth Amendment rights to choose customers and operate his business as he wished." https://en.wikipedia.org/wiki/Heart_of_Atlanta_Motel,_Inc._v...

This is all well-established law over the last 60 years. And with 60 years of people working to tear it down, which appears to be what's happening here.

Further, if you voluntarily take federal money (as almost all schools do) then you must follow federal rules, like Title IX of the Education Amendments of 1972 which prohibits sex-based discrimination in schools. This Hawaiian school does not take federal money so avoids those laws.