I think the issue is more that it's not a very compelling reason to kill a newborn even by ancient standards.

I suspect it's more to do with two identically-minded people being fundamentally creepy and/or dangerous.

If everyone else ultimately acts primarily in their own self interest, but identically minded twins value each other equally to themselves and always cooperate, and see themselves as an in-group of two to which everyone else is an out-group (which may be a natural result of being able to compare all those different-from-you people to someone who's completely the same as you,) then they might be a nuisance ranging to a major hazard to the rest of society.

If Fred and George's mischief making is typical for wizarding twins, it would explain why ancient society wanted fewer of them.