to be honest, I think carefresh smells WORSE than yesterdays news. I've kept rats for 10 years now and have used everything from pine (hey, it was when I first had rats.. we all make mistakes.. 1 rat, 10 gallon tank, seed, and pine shavings.... VERY VERY bad, lol... I quickly found out this was wrong and changed my ways... 10 years ago!), carefresh, yesterdays news, aspen, walnut bedding, ecofresh, healthy pet, ultra carefresh, etc. IMO yesterdays news is by far the best at holding odors. You can buy a large bag in the cat litter section of petsmart, although it's making its way into grocery stores for.. 5 dollars a small bag. while you can get 4x's that much for 10 dollars at a petsmart! Aspen's the cheapest acceptable bedding, but I find it doesn't hold odor like yesterdays news does.
another easy way to keep the cage smelling better, spot clean daily, and change the bedding weekly. you'll find rats will usually pick a corner to poo in, and you can easily litter train them that way using those corner litter pans for ferrets and rabbits. This can be spot cleaned daily to keep odor down. walnut bedding found in the bird section can be used as a safe litter for them, and you can actually SCOOP the poo out of it, like a cat litter box!
Best I've done for rats who've come to me in less than ideal situations... yes, they stink, covered in urine, a PEW one will look ORANGE from there.. I've filled the bathtub with luke warm water, and not too much. so htey can walk in it and be above the water... keep a large bowl or something upside down in there for them if they desperately want to jump out of the water, they won't lunge up your arms and scratch you up (if you do'nt clip toenails, even if you do this still happens). I have used from baby tear free shampoo, to ferret shampoo (too harsh IMO), to just antibacterial soap to wash them with. I usually choose the latter. Their fur isn't about to get tangles, etc, like ours would. Use the soap and that way it also will help with their scabs..
You said you're using ivermectin right? that's good.. when I get mites it doesn't usually clear up for up to two weeks... honestly I wouldn't give them back to her if it's as bad as it sounds. best to get them out of that situation, you know? just hope the girls aren't pregnant (is it THAT bad a place? ack!)