It doesn't apply during war
While there is law against assassination for foreign leaders, there is a wartime loophole. Under U.S. military interpretation, "assassination" refers to "treacherous" or "murderous" killings of individuals for political purposes. Targeting a foreign leader who is also a military commander (such as a Commander-in-Chief) during an active war is often viewed as a lawful combat operation rather than an assassination.
I would think the title "Supreme Leader" would fall into the category of commander of Iran's armed forces.