From the VPC study, the NCVS survey also collected data on the "self-protective" behaviors of victims of violent crime: 235,700 instances involved firearms in 2007-2011, which comes to ~47,000 instances per year, as well as an additional 103,000 instances of victims of property crime (~20,600/year).

From the CDC's 2013 report:

Defensive use of guns by crime victims is a common occurrence, although the exact number remains disputed (Cook and Ludwig, 1996; Kleck, 2001a). Almost all national survey estimates indicate that defensive gun uses by victims are at least as common as offensive uses by criminals, with estimates of annual uses ranging from about 500,000 to more than 3 million (Kleck, 2001a), in the context of about 300,000 violent crimes involving firearms in 2008 (BJS, 2010). On the other hand, some scholars point to a radically lower estimate of only 108,000 annual defensive uses based on the National Crime Victimization Survey (Cook et al., 1997). The variation in these numbers remains a controversy in the field. The estimate of 3 million defensive uses per year is based on an extrapolation from a small number of responses taken from more than 19 national surveys. The former estimate of 108,000 is difficult to interpret because respondents were not asked specifically about defensive gun use.

Also, the category "justifiable homicide" is stated as "the killing of a felon, during the commission of a felony, by a private citizen." (see footnote 1, pg 1 of VPC study) I wish they would be a bit more specific than that, because that reads as if the person being killed had to have already had a felony conviction, and someone who wasn't wouldn't be counted in that statistic. However, I have been unable to find further clarification on the FBI website, so I'm unsure what to think of it.