Tony finds skeletal remains buried just under the surface in the killers back yard. The smell of death would be quite strong, drawing attention unless it was buried deeper.
McGee says "Justified or not it's still a crime". Justifiable homicide is NOT a crime.
Justifiable homicide is self-defense or defense of others. McGee & DiNozzo were discussing taking the law into one's own hands; which is NOT legally justifiable homicide and is a crime.