Honestly, if the 'healthy' one is affected, and not perfectly healthy, I'd put both down. If she was perfectly healthy, or there were several 'healthyish' birds, I might try to fight through it, but not where shes showing symptoms. I keep my birds as livestock and not pets though - so I'm a little more aggressive about this sort of stuff.
I'd then clean the coop as well as I could (bleach, etc) and go fallow until at least spring. Maybe try again with a late spring batch of vaccinated chicks. The vaccine isn't perfectly effective, but it's better than nothing, and it triggers a faster immune response against other strains.
Thank you all for your advice. These are pets which is why the decision is so hard. My sickest one just ate a good amt. compared to what she's been eating and I dug up some earthworms which she gobbled right up. It's a good day. shhh, don't tell my husband who is so done with this!