I guess that "indirect" assassination of foreign leaders is not covered in the order, i.e. bombing a "military" target where the foreign leader might be having dinner.
For example, the bombing of Libya in 1986. Gadhaffi escaped but he got the message. He's been quiet ever since.
Sending an assassination team to only kill Gadhaffi would have been against the current executive order. Of course, the President can sign a new executive order and override the non-assassination order.
And didn't Bush already write one that removed the constraints of that executive order - something to do with "Going after those who order others to kill..." or something like that?