Why wasn't it named KABC? Because its local legend as an original General Electric station (K-General(electric)-Oakland) coincided with GE's ownership of WGY in Schenectady and KOA, Denver. The call letters go back to 1924, and a three-letter call at that.
Actually, network-associated callsigns came fairly late in the radio game. WNBC was WEAF until 1946, almost 20 years after the birth of NBC; WABC belonged to CBS, even during the first 3 years of the existence of WABC (1943 to 46; ABC's flagship was WJZ until the sign was changed to WABC in 1953). I must assume that this reluctance to change had much to do with the fear of losing goodwill that had been built up. In those days callsigns were used more than dial positions to get listeners to remember them.
However, the fascinating story is that KGO was, at first, a flagship NBC station until the early 60s. Remember, NBC "Red" and "Blue" split ... with one of the NBC nets becoming ABC ... and the rest is history ...
At one point it was not unusual for the NBC studios at 111 Sutter to be doing shows for the East Coast, the West Coast, and a local non-network program simultaneously. Here's a link to a good description of what was going on: http://www.sfradiomuseum.com/schneider/nbc.shtml