Are Israel’s targeted killings Halachiclly ok? I recently read an article by Rabbi J. Bleich of YU saying that the six day war was not ok to start because pre-emptive wars are not part of Milchemet Mitzvah since it isn’t considered direct protection. What gives us the right to target and kill individuals who don’t pose a direct threat to us, like a single nuclear scientist?

All rabbis agree that targeted killing of the enemies of Israel (obviously as a national, not "vigilante", decision) is not only allowed, but is obligatory, moral and a good-deed. Rabbi Bleich agrees that wars of self-defense are obviously mandatory and obligatory, and he's not so naïve to think that self-defense is only defined by who fires the first bullet. It is truly degrading and even offensive to the Godly Torah to think that the halacha would childishly have the Israeli commandos wait "patiently" in Entebbe, until the terrorists first started killing the Jewish hostages, and only then allow the surprise raid! My friend, modern war doesn't work that way. By the time a modern gun is fired, many of the hostages are already dead, and it's too late to start defending. If Iran were to God forbid, succeed building a nuclear bomb, it's already too late! No rabbi in the world would think it's not obligatory to assassinate each and every physicist who aids to annihilate the Jewish State as a "rodef", and all agree we are not allowed to wait until the bomb is "on its way" in the air. Our sages expressly command: "one who comes to kill you, you must (!) rise beforehand (!) and kill him" (Sanhedrin 72a). Just as we abort a fetus which even may (not definitely!) endanger the mother, how much more so the Rama quotes the Or Zarua and writes explicitly that preemptive strikes against gentiles even for possible ("stam" = not definite) danger, not only supersede Shabbat (Or.Ch. 329, 6), but even justify sacrificing many Jewish soldiers' lives (the definition of war), and how much more so, justify killing the enemy (which is a mitzva, and not at all considered "murder" or a sin!). This halachic logic is even internationally accepted (although sometimes hypocritically & anti-Semitically ignored when involving Jews), that when an enemy, for example blockades our waterways (as the Arabs did before the Sinai Campaign & the 6 Day War), it's a "Casus Belli" or an act provoking and justifying war, and morally validates "firing the first shot" in retaliation (!) and defense. I'm aware that R. Bleich questioned the First Lebanese War, but cannot believe that any rabbi would issue such an opinion about the 6 Day War, without first checking the historical facts, which speak for themselves. Your question can easily be solved by a little "homework", where you'll find that Israel faced annihilation in 5727/1967, were it not for that pre-emptive strike which you mistakenly question (e.g. you can find online the front cover Time magazine article right before the war entitled: "Israel- The Struggle to Survive", https://www.ebay.com/itm/Time-Magazine-JUNE-9-1967-ISRAEL-THE-STRUGGLE-TO-SURVIVE-Grade-9-0-/264255183269 speaks of evacuating Israeli children to the U.S. and Europe, preparing tens of thousands of mass graves, etc. etc. and you can hear for yourself the Egyptian radio broadcasts, "The Arab nation has decided to purify Palestine from you [Jews]. Pack your bags and flee from Palestine before death reaches you!... Even two hours you will not survive", see: https://www.youtube.com/watch?v=P96YXD0bNmo). In addition, you must understand that even theoretically, serious national issues like war are decided halachically only by the Chief Rabbinate of Israel and the Chief Rabbinate of the IDF, and not by rabbis sitting in New York who may have no idea what's really going on, don't understand the military, and don't pay the price of life or death decisions. Just as R. Moshe Feinstein did not express an opinion on medical issues until he first conferred with R. Prof. Moshe Tendler, how much more so regarding military questions on the safety of the entire State and her 7,000,000 (!) Jews, one is not allowed to posek until he has conferred with the highest level military and political authorities, and not bandy around theoretical wishes, as if the world has already matured out of anti-Semitism and genocidal desires towards the Jews. Yes we believe that God watches over us, but He Himself commanded us that we shouldn't rely on miracles, and make sure ourselves that "Never Again" will we be "Holocausted".