Effective altruism is based on the core belief that all people count equally. We unequivocally condemn Nick Bostrom’s recklessly flawed and reprehensible words. We reject this unacceptable racist language, and the callous discussion of ideas that can and have harmed Black people. It is fundamentally inconsistent with our mission of building an inclusive and welcoming community.
— The Centre for Effective Altruism
I'm arguing not for a "conflict of principles" but a conflict of impulses/biases. Anecdotally, I see a bias for believing that the truth is probably norm-violative in rationalist communities. I worry that this biases some people such that their analysis fails to be sufficiently consequentialist, as you describe.