But I don't think infanticide was ever justified on a "human autonomy" basis

It's difficult to make conclusions about this, because most historical cultures made fairly little effort to support their conventions at all. However, it's certainly been my impression that a lot more cultures were OK with casual infanticide than casual murder. This suggests strongly to me that the view of newborns as people is not universal.

In general, I suspect that most cultures that tolerated infanticide were much lower on the human-autonomy scale than our current civilization (i.e. valued individual human life less than we do).

Probably, but I'd be surprised if most of that effect were to do with anything beyond the fact that infanticide was more common historically than it is today and respect for individual human life is higher today that it was historically. That's certainly not a very strong argument that infanticide being morally wrong is indeed basically a moral universalism.