The reason none were shot is that the IDF never felt like they came to murder and maim. If they were pals, that is exactly what they would be trying to do. That is the reason for the different response from the IDF. Either way, I am sure the government will find and deal with these people.
U.S. says working on initiative to de-escalate Syria fighting, with focus on Aleppo (Reuters)
from the article: Netanyahu calls urgent meeting after rightists attack IDF base