Why not just take out the other hen, and the box? If the box isn't removable, block it off, so Mom can't get back into it. Then you could leave the chicks with mom, and let them have the whole coop to themselves. If you remove the box so chicks can't fall out and get chilled, that removes the most likely hazards.
With my own, I've found that they do better with an open floor instead of a box, to nest in. That eliminates the chance that chicks can be crushed or smothered in a corner, or against a box edge. Without a box, if a chick gets a little too crowded, it just scoots out from under mom, runs around to another spot, and burrows back under her again. It won't get trapped. Then you can watch them perch on top of Mom, and peek out from her feathers. She'll be content and happy, the chicks will be content and happy, and odds are excellent that they'll be fine.
I put lots of loose straw on the floor, put feed and water on low platforms (to keep them up out of the straw, they stay a little cleaner that way. Don't forget the marbles in the water) that the chicks can hop up on, and leave them alone. Once they feather out a little, 2-4 weeks) you can let Mom take them outside. By then they're big enough and fast enough that they're usually fine with the other chickens. And Mom will defend them, too. I just try to let them get a good start first.
While it's true that you can sometimes lose a chick being raised by a hen, you can also lose a chick you try to raise in a brooder.
Nothing is foolproof, when raising baby critters of any kind. Sometimes we lose some. That's just the way it is. Part of that is the law of survival at work, Survival of the Fittest. Losing weaker chicks is sad, but in the long run, better for the flock. If you always save the weaker chicks, over time, you'll have more and more losses, and less fit birds. If you allow nature to eliminate the weaker birds, your flock gets stronger, and over time you'll have fewer losses, and a stronger flock.
