There are some great books on Civil War medicine that you might want to check out. Microbes and Minie Balls and Gangrene and Glory by Freemon are both great resources. Also check out Civil War Medicine by Bollet, and Bleeding Blue and Gray by Rutkow.

From what I have read, the reason amputation was so frequent during the Civil War (compared to other American conflicts) was the use of the minie ball, a type of bullet that would shatter bones instead of going right through them. This meant that instead of the possibility of saving the limb, doctors had no choice but to amputate. This is the main reason for high rates of amputation, not infection, although infection was a symptom of these amputations and many died from this. If you're interested in sterilization techniques and when they came about, look into Joseph Lister, who pioneered these techniques in the late 19th century.