This seems kinda obvious and makes me sad they kept it on the script.

Of course, killing the children has a much more impactful effect, which is what was intended. But it makes no sense.

Ila could just have more children later. And then, would Noah keep killing every girl she'd have? Also, as he talks, he says if it was a boy he'd be the last man on Earth, completely disconsidering she could have more children.

If he wanted mankind to extinguish, the only way would be to kill Ila, as soon as they knew she was pregnant. That was the only way.