And even in your own quote it said that "Sharon personally ordered his troops to achieve" so if you want to have a blame game that the persona responsible.
Again from the same "Orders to inflict heavy damage on the Arab Legion" not to directly kill civilian indiscriminately.
"Civilian scientists working on a military project" - and that's make them a valid target, remember that weren't doing space exploration they were building nuclear weapons!
Innocent civilian die all the time, it's unfortunate and sad but true. But there is a difference between killing for the sole purpose of of killing them and when they are collateral damage - and when it happens Israel regrets that, and remember that Israel tries to minimize it as much as possible, no one is happy when that happens unlike their fellow neighbors.
The MEK has denied any involvement in the assassinations and the existence of any alliance with Israel, and as you said they are no longer on the terror list, it was even lifted in 2009 by the Council of the European Union and on 2012 by the US, MEK is different than what it was in the 70s. I can't say the same for Hamas or Hezbollah, both funded by Iran, with the sole purpose of destroying Israel.
Israel isn't violating the NPT because it didn't sign it. I would think that once there is no threat to the existence of Israel the need to be a nuclear power will be gone. Israel was pushed to that by the continued aggression of the Arabs in the region.