Actually, there's far more fatal defensive shootings than that. The FBI numbers come straight off the police blotter- many defensive shootings are intially labelled "homicide" by the police in the report, even if there is no intention to press charges.
I have read that the percentage of homicides that are justifiable is around 7-14%, and more than a thousand a year.
HCI also uses the gov numbers for self-defense incidents as well- about 80,000 yearly. What they don't say is that this is the lowest number in existance, and the NEXT HIGHEST number is 700,000 a year. There are 15 studies of DGU, with the numbers ranging from 700,000-2,500,000. Read Kleck's "Targeting Guns."