I think the argument here, if I may be permitted a summary attempt, is:
(1) Yes, children are taken from parents when those parents are arrested
(2) But domestically, that decision is made for practical reasons
(3) Here, the apparent purpose of the “zero tolerance” rule is to punish the parents for their lawbreaking, as opposed to an unintended but necessary secondary effect
So when we put bracelets on a domestic violence arrestee, we’re doing so to protect his victims. We don’t want the kids to suffer, but we accept that suffering that comes from seeing a parent taken away because there are no better options available.
Here, there are better options available. There are even, I dare say, better options available if you want to continue to criminally prosecute illegal entry with zero-tolerance. The choice to do things this way is not an unintended secondary effect: it’s part of the plan.
I’d suggest that this is a bad plan for that reason, amongst others.