I suggest you let it go. You wanted a critique, and you got one. You don't have to like the critter's attitudes or biases, but they are also free to mislike your characters. Surely you don't want to fall into the category of betas you describe in the sentence I've bolded above. Readers will be viewing your novel through the eyes of their own prejudices and preferences. You will have no opportunity to express your "concerns" to them. That's just a writer's cross to bear.I've had the betas where I'd give dozens of comments per chapter, only to receive "oh, it was good" as the only comment for mine. And I've had the betas who needed to write essays to defend their novel from my critical comments. It's never fun.
I'm also in a situation with a Beta right now who has made some comments that seem bigoted to me. I have a female character who is sexually active with multiple partners and this reader has called her a "slut". In a scene where it comes up that she is not interested in drugs, the reader basically commented "she's already a slut, why wouldn't she do drugs? Morality is an all or nothing thing." I also have two brothers in this story, one a gentleman/sweetheart, the other a selfish troublemaker, and when it's revealed the gentleman is actually gay, the reader said "Oh, the other brother should be gay, it'd make more sense."
I'm wondering if I should try to bring up my concerns with them at all, or try to take it in as a "different perspective." Curious to hear what other people would do in this situation.