Let me ask a military question...
... is it better to defeat an enemy by eliminating them from the bottom to the top -or- from the top to the bottom?
I'll give you the answer... the latter of the two. Have I been to West Point or anything like West Point? No. I have studied war though. I am not surprised that some would see the glass as 1/2 empty if this story were true. That is the political nature of the beast.
Leaders make decisions. Leaders know more about an entire army (theirs and their enemy), organization or felonious killing machine (this is a good description for al qaeda). Leaders provide emotional support. Their presence means a lot to those who fight under them. It is always a greta thing to nab a top-dog. For instance, some may know this story...
Admiral Isoroku Yamamoto
Having lived and studied previously in the United States (Harvard grad), Admiral Isoroku Yamamoto of the Imperial Japanese Navy was not eager to enter into war with that county. Ordered into combat by his country, Yamamoto was the most reluctant of warriors who seemed to know that it was his destiny to fight and die for his Emperor in a lost cause.
One of the great advantages that the United States enjoyed in its war with Japan was the cracking of the Japanese code. This gave the U.S. advanced warning of impending Japanese operations. One such operation was a visit by Admiral Yamamoto to the Japanese base on Bougainvillea. Allied intelligence intercepted and decoded a message describing the visit, and the 13th Air Force decided to welcome him. Even the highest ranking American military commanders felt that to give a direct order to assassinate an enemy commander was above them, and the authorization for the mission eventually came all the way down from the office of the American presidency. On April 18, 1943, one year to the day after the Doolittle Raid on Tokyo, 18 American P-38s from the 13th Air Force launched from Guadalcanal, flew to Bougainvillea, found the Admiral's flight, and shot down his plane killing him.
Admiral Yamamoto’s death was a tragic blow to Japanese morale. Many commanders felt that they had lost Japan’s greatest naval strategist, a realization to which several commanders would never recover from.