If we had a time traveling machine, we might be able to observe the babies as they grew up in their own time to see when they first started being evil. Then when we take him or her to the EBO, we will be able to make sure that no similar situation ever happens. I suppose that we could just change what happened so that the evil babies or evil kids do not become evil. This might be easier then raising them in an orphanage (alternative in case the orphanage gets to crowded?). However, this won't work if the babies were born evil. Then we would have to construct a brain washing facility in the orphanage to make the little babies think they're good.
Would the caretakers send the babies into the past or future when in one era of the EBO is to crowded with evil babies? Or would the EBO have enough room for all of the evil babies?
I doubt that a baby is born evil. Think about yourself. All the things that make you you. For example, I love to read. Well, my parents read me stories, and told me stories, when I was a child. I learned to read when I was four because the resources were available to me. I love to read because it's been there my whole life. Or, say, think about your friends. You all influence each other. One person likes some music, they share it with the others and they agree. And then you know and like that music.
I really do think that it's the events in your life that make you who you are. Therefore, if "evil" people were raised in a totally different environment, they wouldn't grow up to be that evil person.
So I don't think it matters if they're all in one place or in different places, as long as they're raised well-- and to not be evil.
*Very late reply*
I don't think that you're born evil. I think it's how you were raised, who did the raising, what you were taught, what you endured and were shown that shapes you.
Plus, look what orphanages did to Voldemort. Do we need that?
But once upon a time I thought that Santa Claus was real so in the offchance that I am wrong, here is my personal plan:
I think we need to test out whether one evil baby in a good baby orphanage gives a good result. If so, then let it be! It minimizes damage.
If not, I think that we should try a foster care approach so that the evil babies do not know what incredibly evil power they have if they plotted together, and the feeling of home and belonging will be beneficial. That basically means that John, Hank, Katherine and The Yeti should raise the evil babies because they are good people who are nerdfighters basically (then there is the possibility of more mini-Henrys in the world, which is always a plus even if they won't have the right genetics to be like Henry).
And if that fails, we need to buy a remote Tibetan castle with long iron fences and a good supply of barbed wire.
Regardless of whether or not an evil baby orphanage is a good idea, it IS going to be card game from the fantasy Wyrd Miniatures. They're kickstarting it right now.
I think one of the points of the EBO was to take the "evil babies" out of the terrible conditions that they were born into and raise them separately so they all grow up good or something like that. I think John said something like that in an early video.