Without opening a discussion about the conflict itself or justifying anything in the article, I will say that as someone who's been on the receiving end of an adult throwing 5-10 pounds rocks at full strength at them, I truly think you're underestimating the deadly damage it can cause.
This isn't a toddler throwing pebbles, such a rock hitting a human will break bones on contact and can absolutely kill of it hits someone's head
Oh I know rocks CAN be deadly. But so can lots of things. From the info in the article they were throwing rocks at cars, not IDF forces who are undoubtedly armoured to the teeth for greater stopping power than rocks.
Just seems strange to shoot someone for not obeying when they aren't directly threatening you, but the article is a bit light on actual details. Being the source that it is, I don't think they would hesitate to highlight the IDF were defending themselves if they actually were.
The actual procedure is actually calling the suspect to stop, first in Hebrew, then in Arabic, if the suspect does not stop then the soldier loads a round in the chamber, next a warning shot to the air, and then shooting at the suspect's legs, all the while calling for the suspect to stop.
IDF has a tendency to... Expedite this procedure.
It doesn't help that the ultra-religious, which makes up 99% of settlers, hate the IDF almost as much as Palestinians. The fact they weren't throwing rocks at the troops surprised me the most.