Hen with upper respiratory disease

This morning when I went out to feed the chickens I noticed one of my 1+ year old speckled sussex hens (a July 2010 hatch date) "growling" at me. I soon realized that it was not growling, but rather wheezing/gurgling congestion. I work for a vet, so I took her to work with me. Admittedly, the vet I work with knows very little about chicken medicine (and admits it, if I weren't an employee she probably wouldn't even have tried looking at my girl) but she did not see anything particularly abnormal on the physical exam other than lots of upper respiratory noises. No swelling, no discharge, no lesions. She has a bit of a funk to her, but I suspect it is from the poop on her back (clearly she is not one of the girls that sleeps on the top rung of the roost ladder). She is still bright, alert, and reactive and still eating normally. The only symptoms I've noticed are the wheezing/congestion and the occasional sneeze. They are markedly worse when she is stressed/excited, such as this morning when I was bringing treats or this afternoon during her exam. The rest of the time it is subtle enough that it is hardly noticeable. She is also having some very runny droppings, but I am guessing that is probably due to the stress of being plucked from the flock and taken to the vet.

Because she is not really a pet, we went conservative with the diagnostics, just a swab of the chloanal slit and cytology on a nasal flush. Both showed a low amount of bacteria, primarily spiral gram negative with a few gram positive cocci and rods. My vet sent me with a script for doxycycline (I suspect baytril would have been a first choice but she has read on VIN that it is illegal to use in food animals and because we eat the eggs and, eventually, the chickens themselves she doesn't want to venture into the grey area of using it for a backyard flock). But before we fill it I would like some input from those who have dealt with upper respiratory diseases in chickens firsthand. I am not against treating, but in the end all of our chickens will end up in the stew pot so it isn't really worth it to me to spend a lot of time and money treating something that is going to be a chronic or untreatable problem. Then there is the quality of life concern for a lone hen in quarantine in the house for 2-3 weeks or more in the middle of winter and the stress of reintroducing her to the rest of the flock. I don't really want to cull, especially since she seems otherwise great and is very personable, but I am having a hard time deciding how worth it treatment is.