How difficult would it be to code in a third option in The Pitt where instead of taking or leaving Marie, you could eat the baby for a Rad Immunity Perk and the hostility of EVERYONE in The Pitt?

Exactly this mod has already been made. Find it on fallout nexus.

It is indeed on the Nexus.
A point of reminder though, discussion of Baby killing/mortality is not allowed on this forum and this thread is likely to be locked soon.

Wow that is pretty screwed up, eating a baby...

I'm not sure but I am sure you can't discuss it here. We don't allow discussing of child killing much less eating them.