Each question must be listed separately. I can answer only one. Also, please note that this is my opinion, as your answer should be when you address it. With opinions, there are generally no wrong answers unless you cannot support your reasons with examples from the story.
I believe that the Emperor is not justified in executing the inventor of the flying machine. Forgetting for the moment that he is an emperor who can do as he pleases, he sees himself as someone whose job it is to protect his world as he knows it. This is not to say that his actions benefit others: I believe they benefit only the Emperor.
When the story concludes, I believe the Emperor realizes his folly in trying to keep the machine a secret by killing the inventor, burning the machine, and "silencing" all those who have seen what it can do. The Emperor realizes that if the birds had inspired this man to create a flying machine, that it is only a question of time until the birds inspire another inventor.
Philosophically, I cannot believe it is any person's right to prohibit or control beauty in this world. However, I believe it is also impossible in that beauty can be found in a child's face or the center of a exquisite rose. As with anything that is new and good, someone will find a way to exploit it or use it in a negative way, as seen with the Internet all the time.
As the Emperor tries to stop his world from changing, it is as futile as trying to control the wind or the ocean. The very nature of change is that it never stops...changing.