Nonlethal crowd control has been around a very long time and is routinely used on numbers in the few hundreds as Israel was dealing with. What we see here, as well as in the case of the Turkish flotilla is that Israel, when congronted with protesters uses lethal force as a first option. They do this for two reasons. (1) lethal force acts as a deterrent to further "provocations" (2) Israel is never penalized or held responsible for their actions when they kill unarmed protesters. This goes back for many years. Israel kills these poeple and then blame their victims or some third party. This is Israel's standard behavior and standard response to criticism.
Opposition leader Isaac Herzog calls on government to allow Syrian refugees into Israel (Haaretz)