I know he also said that he has the capability of killing someone in self defence (not murder) but Kivas Fajo said that he wasn't going to harm Data
Fajo may not have had any ill intent against Data specifically, but that's not the point. Fajo clearly had intent to harm OTHERS, and specifically threatened to do so ("I'll just kill someone else," I believe he said).
So Data was naturally justified in firing at Fajo. Killing someone because they are a danger to other people (other than yourself) is still not murder.