She will probably be fine, but honestly, it will be in no way due to the stitches. I am not trying to be condescending. I have a degree in microbiology and I know like I know the sky is blue and the grass is green, that wounds do better when open to the air. There are three things that bacteria hate most in this world, even worse than antibiotics: oxygen, light and a lack of humidity, its their kryptonite. Fly eggs can be prevented with a simple dusting of wound powder. So she has a scar, I could think of a lot worse things. Her trachea would have been fine just covered up with some nitrofurazone.
There is a reason that medical science has progressed from the dark ages where people used thread and sterilized their sewing needles with a flame. If you insist on stitching wounds, keep two things on hand. A sterile suture kit, and a bottle of penicillin. You can buy a suture kit on
ebay and your local feed store should have the penicillin.
A note on maggots: maggots will keep a wound clean and free from infection. Doctors in burn units are now using maggots to clean the necrotic flesh from people with 3rd degree burns on significant portions of their bodies. The job that maggots do can prevent a person from expiring from DIC (disseminating intravascular cooagulation) and sepsis. Never underestimate the power of a maggot. I once found a week old wound on a cochin (I had been away and a friend was watching him), it was the most horrifying thing I had ever seen at the time. I felt the wound when I picked him up and when I turned him over it was like a horror show entitled "Night of the Chicken Maggot Butt". I was up until 3a.m. cleaning maggots out of his butt (the wound was just behind his vent). When I brought him into work the next morning, the vet I worked for said it was the cleanest wound on a chicken that he had ever seen, no necrosis, no infection, no need for antibiotics. Maggots aint so bad.