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It's not coccidiosis, they were too young for that to be an issue yet. Bacteria is possible, if the umbilicus was not closed yet and was exposed to bacteria at that point. Those kind of infections spread rapidly in the chicks abdomen. I've had broody hatches not go well in the heat and...

Sounds like she's doing well. Sometimes greenish in the droppings is from bile if they aren't eating normally. As a broody who is only eating sporadically, might be all that is. Typically a sick dropping will be more yellow or yellow green.

Cephalexin is usually given for 7 - 14 days. If it's healing up on it's own and the bad smell is gone, you may not need it. And, yes, cephalexin can disrupt the gut flora. When using it I keep a close eye on droppings, if they start looking abnormal, I usually lower the dose.

I have used the 30 - 50 mg/kg orally four times a day with good results. You may need to clean the wound again, if pus regenerates (the white cheesy stuff was pus), until the antibiotics start to work.