I support Israel's right for freedom and to defend itself (Especially against Iran, Syria and Yemen), but calling the Palestinian-Israeli conflict 'as morally clear as wars get' is an incredible over simplification. Civilians on both sides have been killed and the Palestinians have their backs to the wall after decades of losing land to resettlement and the more recent sanctions on fuel, foods and medical supplies. That doesn't justify rockets being shot into Israel though. It's very complicated.
And really, a TEN YEAR OLD article is your smoking gun of the NYT's apparently broken moral compass? If they're as bad as you say then you should be able to cite many more recent articles.