Moral reasoning is like arithmetic. Granted, our empathy and fairness are evolved instincts, but working out the relative rightness and wrongness of particular actions is a feature of reasoning. It's no different from figuring out how to build a building so that it won't fall down. You look at who owes what to whom, and who got what benefit from whom, whether they earned it, or what they reciprocated with.

Notice all those economic terms. Economics is probably the field most closely related to ethical philosophy. With money we make judgements of value. Those values are based on our desires-- our instinctual drives-- sure. Granted. But we can still weigh things against each other in each transaction. We can still count money with our higher brain and not rely on instinct.

In the same way, you figure out that stealing, for instance, is wrong because one side of the transaction is missing. We exchange reputation like currency, and blame is debt. We say an ex-con has "repaid his debt to society." One may as well ask why we "evolved to think that 2 + 2 equals 4" as to ask why we "evolved to think stealing is wrong". It's because when you take two dollars and another two dollars, they really are four dollars. Saying it's three really is bad math. Building a building in such a way that it falls down really is bad architecture. Stealing really is bad ethics. And so on.