Let's say we evolved from Lions

[Angrboda]

Let's say we evolved from Lions and eventually became a sentient form of Lions.

And suppose the instinct to kill children of new wife came about when marrying. Suppose in this scenario, the instinct to fight one another is gone, but the instinct to kill the children of a divorced or widow new wife, was so strong, it would be very hard to control rage levels of the male looking at the children and very hard to avoid the instinct to kill the children.

I don;t see why we needed to imagine that we evolved from lions to set this one up.  We have many compelling contra-moral instincts as we are, more than a few of which involve killing.   

Exactly. The impulse to rape arises out of natural drives and inclinations, yet we feel compelled to avoid and forbid it, likely due to factors which aren't entirely within our ability to rationally determine. Like altruistic acts and kinship selection, the relationship between nature and human nature is seldom as explicit and readily tangible as we would like. In addition is the question of whether there are moral facts independent of any possible evolutionary explanation, and whether those particular independent moral facts are relative to the particular species under consideration. Then it becomes a simple question of whether it is objectively wrong to kill the lion cubs as a lion, which, unlike the evolutionary line of thinking, is not directly predicated upon what is natural.

So, ultimately, it's an empirical question which depends on the particulars of the species involved, the relationship between sentience and morality, and the ultimate nature of morals.