First, since the trespassers are Lebanese and Syrian primarily (the majority of the crossings or attempted crossings occurred in the Golan Heights, which by the way, were not part of the land given to Palestine in 1947 and belong to Syria, not Palestine, until the Six Day War), there is real danger to Israel because those are nations that do not recognize Israel and have no diplomatic or consular relations with Israel. As a result, Israel cannot know the intent of such protesters, many of whom were screaming to "Free Palestine from the River to the Sea" and were marching as part of a group condemning Israel's very creation. As the IDF cannot know the intent of such protesters, whether they are armed or whether they are acting under the orders of the Syrian military, one cannot simply presuppose peaceful intent on the part of persons crossing the border. Syria maintains an active state of war against Israel, so it is reasonable to assume that any border incursion is consistent with that military stance.
There is, however, another issue at play here. A large scale border crossing has great political significance and can have a significant role in escalating military conflict. In 1975, when Spain agreed to withdraw from Western Sahara following Francisco Franco's death, three competing interests sought to control Western Sahara: Morocco, Mauritania and Sahrawi Nationalists (later POLISARIO). Upon Spain's departure, Morocco's King Hassan organized "the Green March," an incursion by 350,000 Moroccan civilians across the Western Sahara border, by which Morocco would take functional control of the disputed territory by simply sending a substantial number of civilians into the territory. While some negotiations later restricted the Green March so that the civilians only marched down to the capital of El Aaiun, the very threat of the Green March gave Morocco substantial leverage and was instrumental to preventing the success of Western Saharan natonalism in 1975.
The situations are not identical, as the border crossings here have been of a small scale so far. They are, however, very dangerous. Arab states have always accused Israel of "changing facts on the ground," a term used to refer to essentially every economic or construction activity undertaken in "Palestine" since 1949. While Israel has blossomed into a successfully democracy with significant economic development, the Arab states and the Palestinians welcome the opportunity to "change facts on the ground" through border crossings, much the way that King Hassan did in 1975. Because the Israelis are held to such high moral judgment in the world, Israel would be at great risk no matter what it did to border crossers. Such activity must be dealt with swiftly and decisively.
There is another amazing aspect here, highlighted in this article, in which the Syrian government condemns Israel's response to the Nakba Day protesters. I am not even going to point out the irony and hypocrisy of the Syrian government making any statements about another nation's dealings with protesters. I don't recall the Syrian government making such statements about Egypt, Libya, Bahrain or Tunisia. Moreover, given Syria's tight control over its military and political establishment, it is highly unlikely that the people who crossed the border into the Golan did so without explicit authorization from Damascus. Considering Syria's present domestic unrest, there is little reason to believe that the Syrian government did not orchestrate this march to divert attention from its own unrest.
On this Nakba Day, I would ask my readers to look back at my posts about what Nakba Day means for the potential success of the peace process. My central thesis is that Nakba Day marks Palestinian rejection of any state of Israel and proves that the conflict is not about any particular border issue, but is an existential discussion about Israel's very existence. Second, I think it is prudent to remember what would have happened had the "Nakba" never happened. Considering that Jordan and Egypt took and held Gaza and the West Bank for 19 years until Israel took those territories, there is no reason to believe that Israel's neighbors had any interest in seeing a state of Palestine. If they had, then a state could have been established within the West Bank and Gaza Strip any time between 1948 and 1967 without Israel's consent or input. But it never happened, because the other Arab states never wanted to see a Palestinian state in land that they felt belonged to them. Now, those same nations hypocritically use the Palestinian nationalist cause as a way to attack Israel even though they have never had any interest in promoting such nationalism when it came to giving the Palestinians land or political rights within their own nations.
How long can we continue to deceive ourselves into believing that Palestinians want peace when everything they do shows otherwise?