This article, written before Monday, seems to do a good job at thrashing out the questions surrounding the legal measures available to Israel in attempting to prevent breaches of the fence:
Is Israel Justified In Shooting Protestors On Gaza Border?
https://forward.com/opinion/398307/is-israel-justified-in-shooting-protestors-on-gaza-border/
This is the crucial bit for me:
"even if the marchers are civilians taking a direct part in hostilities, the 2009 guidance document insists that targeting them with lethal force would be unlawful if other, less harmful means of neutralizing them are available. What this means is that Israel may only use live ammunition against protestors approaching the fence if it can demonstrate that the marchers cannot be stopped from crossing the border fence through any less-lethal crowd control measures.
Having failed to meet these conditions and show the “Great Return March” is part of a military operation, Israel should rather respond to the marchers with law enforcement measures, which are not governed by the laws of international humanitarian law (the laws of war), but rather by the laws of international human rights.
Under the law enforcement paradigm, the default manner of responding to violent riots, including riots in border areas, should involve methods of crowd control (such as tear gas, water cannons or rubber bullets) and not live ammunition. Only when the rioters present an imminent risk to life of limb can lethal force be resorted to, and even then, only if no less harmful means for neutralizing the risk is available. Note however that under this paradigm, Israel is entitled to take a variety of law enforcement measures, including detention, and multiple non-lethal alternatives, to protect its legitimate security interests, including the protection of the integrity of its borders.
Lethal force can be used against civilians participating in marches only as a matter of last resort and only against armed militants posing a threat to Israeli soldiers or civilians. The images that emerged over the past week and a half showing Israeli snipers targeting unarmed individuals retreating from the border fence back towards Gaza with lethal force, suggest, absent further explanation, an unlawful use of force."
It seems unlikely to me that, even putting aside the cases where protesters were shot while back from the fence, Israel can plausibly show that lethal measures were the
only means available to them to prevent breaches of the fence, except perhaps in cases where explosives were being planted or where protesters were armed and preparing an attack on soldiers (which would remove them from the question anyway).
On the other hand, I wonder if official membership of a hostile movement such as Hamas or PIJ would alter the reasoning in any way, given that they explicitly exist in a state of war with Israel? In that case, could their actions be deemed part of a military operation, but not their fellow unaffiliated protesters who may be carrying out identical actions?