This is referring to him physically picking up the child. Like father's usually do. Not some weird mpreg foreshadowing. Although perhaps I'm wrong and the author is going for that anyways. I think it's more likely about the concept that people in relationships have a uncanny ability to...
Deuteronomy 22:5. It was said before, I'll say it again. Usually this wouldn't be an issue, but if this manga is about a Christian sister (as seems to be the case with the traditional Catholic garb) then this wouldn't make sense.