Rightly or wrongly, Israel sees a nuclear-armed Iran as an existential threat. In the face of their possible destruction, the question of the morality of killing scientists that personally don't deserve it doesn't really enter into their calculus.
Somewhat uniquely among countries thought of as "Western", Israel has long had targeted killing programs in the Mossad, Shin Bet, and earlier intelligence agencies which they've used for various purposes, starting with vengeance for the Holocaust on escaped Nazi war criminals, and continuing to the present day as we see in Iran.
I don't think you can look at this and understand it without understanding the mindset of the Israeli people and leadership. Not 75 years ago a concerted effort was made to wipe their people from the face of the earth, and that atrocity was followed up by immediate and continuous aggression from Arab and other surrounding powers through the early years of the Israeli state. Surrounded on all sides by powers that at various times have outweighed the Israelis militarily, they have taken whatever actions they thought necessary to continue their existence. I'd argue they want too far many times, but you can't question their purpose: to survive.
If you want to read more on this, a really good recent book on the history of these programs is Rise and Kill First by Ronen Bergman, who talked with many of the leaders of the intelligence agencies that carried out such actions.
I've heard it even simpler as just "Rise and kill first" - There is a book about the Mossad with it as the name
https://www.amazon.com/Rise-Kill-First-Targeted-Assassinations/dp/1400069718
Hey there. Definitely check out Ronen Bergman's Rise and Kill First: The Secret History of Israel's Targeted Assassinations .
It’s the title of a recent book on Israel’s targeted killing operations.
https://www.amazon.com/Rise-Kill-First-Targeted-Assassinations/dp/1400069718
A couple of books that caught me off guard, might open your eyes on the whole issue and how "baseless hate" doesn't really exist. Lobbies do a great job camouflaging the mammoth in the room... but this is where it all starts. Make up your own mind after doing research, reddit discussions can only take you so far... Don't be afraid to use discernment and weigh all sides. Good luck!
https://www.amazon.com/Rise-Kill-First-Targeted-Assassinations/dp/1400069718
https://www.audible.com/pd/The-Ethnic-Cleansing-of-Palestine-Audiobook/B077KDZRCX
There may be some clues in this book:
https://www.amazon.com/Rise-Kill-First-Targeted-Assassinations/dp/1400069718/ref=nodl_
Rise and Kill First: The Secret History of Israel's Targeted Assassinations
https://www.amazon.ca/Rise-Kill-First-Targeted-Assassinations/dp/1400069718
I recommend an awesome film: Munich; and a terrifying book: Rise First and Kill.