As a student of moral philosophy, I've thought long and hard about this. Yes, we're not entirely rational. And yes, Haidt argues that we're 90% chimp, 10% bee. You're right, for a very long time, Western philosophy treated questions about morality as a science. It's only recently that moral philosophers criticise this history.
On a side note, regarding veganism. I have this "argument." That the strongest objection to killing and eating meat is to appeal to our sympathies. We continue to kill and consume meat because we're psychologically isolated from the bloody process of acquiring meat. Put people into the position where they have to source their meat from start to finish, very, very few have the guts to do it. That said, I've killed just to get my protein, so I'm probably ready for this.