Hi, and thanks for requesting me!
Whiskey was not used as an antiseptic during the Civil War. In fact, antiseptics weren't even discovered until 1865, which was the final year of the War.
Not only weren't the surgeries antiseptic, but one surgeon is quoted as saying, "We operated in old blood-stained and often pus-stained coats, we used undisinfected instruments from undisinfected plush lined cases. If a sponge (if they had sponges) or instrument fell on the floor it was washed and squeezed in a basin of water and used as if it was clean" (http://members.aol.com/cwsurgeon0/cwsurgery.html). Sugeons did not wash their hands between procedures, and usually used their fingers (covered with the previous patient's blood) to probe inside new patients. Their coats were stained with pus. (http://members.aol.com/cwsurgeon0/generalinfo.html)
Anesthesia was actually in use during the Civil War. Alcohols, such as whiskey, were administered to patients prior to the initiation of the anesthesia (usually ether or cholorform). The alcohol helped calm them down. It was discovered about 20 years prior to the war, and got its first real test during the War. Here is a link about that: http://home.nc.rr.com/fieldhospcsa/Anesthesia.html.
According to the National Museum of Civil War Medicine, whiskey's main medical purpose during the War was to prevent shock. (http://www.civilwarmed.org/exhibits.cfm) I called the museum, which is located in Maryland(NNN) NNN-NNNN, and spoke with Terry. She agreed with my research above, and explained that germ theory wasn't established until the very end of the war. She did say that whiskey was used, but not specifically as an antiseptic.
Joseph Lister (http://en.wikipedia.org/wiki/Joseph_Lister), the man who Listerine is named for, used carbolic acid as the first antiseptic in the mid 1860's.
I hope this helps. Let me know if you need any more information,