It was a decision President Biden didn’t want to make. He had warned Israel nearly two months ago against a full-scale assault on Rafah, the Gaza city whose population had swelled to more than one million as Palestinians sought shelter from the fighting. Finally, Biden took a step he had long resisted. Last week, officials say, he put a hold on a pending shipment of 2,000-pound and 500-pound bombs to Israel, an almost unheard-of show of displeasure with a Middle East ally that Biden hoped...