Why are apostates executed and how is this compatible with freedom of belief?

I know this question has been asked before, but I have to search for the proof. In Islam, why are those who apostate from Islam executed, while Islam is based on the free will and freedom in choosing religion? What about those who are born Muslims yet are not convinced? And even Qur'an doesn't say to kill them, and Allah guides whoever he wants. And I am not even sure about the hadiths from the prophet (PBUH) as he never killed an apostate in his life nor he ordered any one to kill them? Any idea if it's right to execute the apostates? And if it is right, why?