I didn't realise until reading the Stuff article that this sort of thing happens quite a lot, or has at least happened several times recently (according to the last 3 paragraphs).
I haven't been up Ngauruhoe but is it a reasonable suggestion that it's the popularity that causes so many dislodged boulders near routes where they'll hit people?
I am suprised it doesn't happen more often. I often see it in tramping club parties where the groups are larger and sometimes get spread out. You have to remind people to be carefull. It is best to concertina the party up so that there is less time for a rock dislodged by the front person to build up speed before it gets to the people below. Also when a rock is dislodged then the person needs to yell out "ROCK!" immediately to warn people below. Neither of those things come intuitively so it is up to the party leader to remind people.
In the case of Ngauruhoe it is likely the rock was dislodged by another party higher up the mountain. This guy was unfortunate in that it seems that he tried to avoid it but the rock deflected off something at the last minute and hit him.
Every time I've been on Ngauruhoe I've seen dislodged rocks hurtling down the mountain like missiles. One of the problems is that people try to climb up the scree slope that others are scree-running down. The safer option is to climb up the rocky outcrop to the left of the scree slope as you look up. It's easier too that trying to ascend scree. It's always going to be a potential problem though as there's often people above you [there can be upwards of 100 people on the mountain on a good day], and the rocks are easily dislodged, and the best thing as pmcke said is to yell "rock'! to warn others.