No, I believe it does not matter, civilians should never be a target when it comes to military missions. I may be biased because I am military, but that seems just wrong. Just because a group of civilian are banding together trying to make a point, they are usually bystanders that little to any say the going on of government.
Civilians should never be the target of military action. Though many like to consider civilians to be government supporters, based on a number of assumptions, civilians are often against the military campaigns of their nations, but are simply innocent bystanders, powerless to change the situation. Civilians should never be targeted, even in the face of Apartheid.
Civilians were directly targeted and killed through a campaign of violence. For 'freedom fighters' and people fighting for political equality/human rights this is not acceptable. The government were oppressive and violent, not the civilian population. To say they won and beat apartheid - the violence only caused set backs. Mandela essentially undermined the ANC leadership by partaking in secret negotiations. He was convinced they would refuse and only continue to increase violence and civilian deaths. (sourced in part from his autobiography).