Ha, maybe you'd like to include the very next line from the wiki article:
"UN observers noted that they observed bodies near doorways, and bullet marks on the doors of demolished houses, and later concluded that residents may have been forced to stay in their homes due to heavy fire.[10]"
I get that Israel has their own narrative of events when it comes to Qibya, but if you would read the article, you'd see that it wasn't an isolated instance but the end result of several months of punitive raids by the IDF and civilians with the specific goal of targeting civillians. And yes those orders came from the top of the government: "Defense Minister Pinhas Lavon gave the order, in coordination with Prime Minister David Ben-Gurion." The international consensus on what happened in Qibya is pretty clear.
"Over the year leading up to the raid, Israeli forces and civilians had conducted many punitive expeditions, causing destruction of infrastructure and crops and many civilian casualties against Palestinian villages, with Latrun, Falameh, Rantis, Qalqiliya, Khirbet al-Deir, Khirbet Rasm Nofal, Khirbet Beit Emin, Qatanna, Wadi Fukin, Idhna, and Surif being the most notable examples"
MEK and Israel can deny involvement all they want, and you're correct there's no way to prove what actually happened, but the US intelligence services seem pretty damn convinced: http://www.theatlantic.com/international/archive/2012/02/isr... And by they way, one of the scientists was gunned down while driving home with his wife and kid after picking them up from school. That doesn't seem like trying to minimize civilian casualties to me.
MEK is funded by Israel with the sole goal of destroying Iran. Maybe if there was no threat to the existence of Iran they wouldn't have needed to pursue a nuclear program.
You're right the NPT not violating it since they didn't sign it, doesn't mean that there's not a double standard in the way we treat Israel's nuclear program. It's pretty inarguable the Israel has specifically targeted innocent civilians and funded terrorist groups, both of which you gave as reasons as why Israel should be allowed to have a nuclear program without that same sort of scrutiny it's neighbours undergo.