Were a group of international activists to come to Washington DC to protest the war in Afghanistan, it would be a headache for the US government. It would also take a certain amount of mishegas, especially if the protesters were not Iraqi nor affected directly in any way by the war. But would the US establish Army command posts at Dulles airport to prevent them from coming? Most likely not, since it would be a waste of military resources on a non-security threat.
It is simply bad security policy for Israel to divert military resources to a political problem. Such steps are only the latest in a line of attempts by the current government to use the IDF as a shield for some of its more short-sighted policies. Doing so escalates the issue rather than burying it in the 24/7 news cycle, and diverts resources from the very real security threats the state faces. Police and army resources would be much better put to use in cases where Israel faces real security threats and challenges to public order and safety. With regards to the protesters, the government must stop blaming delegitimization and hiding behind the state security apparatus. Policy shifts are the best way to prevent continued protests which are a political liability to the State of Israel.