You can say their boat, their rules, but if the discrimination were against another special interest group - women, blacks, a religious minority, etc..., I doubt support for the boat's right to discriminate would be quite as strong. Granted, you don't have a choice about whether to get an SDI certification to be black or a woman, but there's at least a tenuous analogy there.
Seriously?
If a dive operator believes that a specific practice is necessary for safety, and it can cite reasonable sources for that belief, you think that is the same as saying they will not allow people of certain ethnicities to dive with them? I don't even see the most remotely tenuous analogy there.
Whether you agree with it or not, there is a bona fide reason directly related to safety for a dive operator to enforce such a policy. It is not a discriminatory prejudice that is based on nothing but prejudice. They have their own livelihoods at stake, and it is possible that their insurance carrier has insisted upon such a rule.
When I was in Australia, I was required by local law to carry a snorkel. I didn't like it, but I stuffed one in a pocket anyway. It was not a big deal. I can comply with such rules without needing to make a big fuss about it. I feel the same way about buddy requirements. My wife does not dive, so I have done many hundreds of dives with insta-buddies of varying degrees of quality. In most cases, I met very fine people I am glad to have met. In a tiny handful of cases, I would have been better off solo. So what? To me it is like the Australia snorkel regulation, and I can live with it easily.