If you were a Captain of an ISD at Endor, you'd have no incentive to bother destroying the rebels. Once the Emperor was killed, you knew the Empire would collapse so you'd bugger out back to base and see if you could negotiate a way out of the mess you suddenly found yourself in. In other words, you'd be in a much better position to bargain with the New Republic if you didn't massacre what was left of the rebels. Heck, you might end up with a commission in the New Republic navy. As soon as one ISD fled, the others would follow.
I am going to use mondern day as an example.
If the Predident
(edit: or Battle Commander
*For you Eyeless1
) of the United States was assassinated, would the US then surrender to whomever did the assassination? More likely, the next in line in the Chain-of-Command would then be sworn in and the US would continue fighting. That is the whole point of having a Chain-of-Command.
It is a bit thin, but moral and lack thereof can do crazy things to a fighting force. There are numerous real-world accounts of a superior fighting force surrendering to a inferior one due to a complete loss of moral.
I agree that with the destrustion of a SSD, and witnessing the destrustion of the DS knowing that both the Emperor and Lord Vader were both on board at the time (not to mention the Zhan explaination) would be terribly demoralizing and even though, yes mathmatically the remaining forces of the Empire would most likely be able to mop up the rebellion, real world history as shown us that moral is a powerful thing.
Edited by catachan23