[Bukhari 9,84,57] Ali ordered that some atheists brought before him be burnt to death. Upon hearing this, Ibn Abbas said, “If it were me, I would not have ordered them burnt. Mohammed told us, ‘Don’t punish people with fire. That is Allah’s punishment.’ I would have done as Mohammed instructed, ‘Whoever turns his back on Islam, kill him.’”
As far as the freedom of speech is concerned, there are multiple examples in the Trilogy, especially in the Sira, which show that Mohammed killed those of his followers who had criticized him or openly doubted Islam as the only true religion. Let us consider at least one example from Ibn Ishaq’s Sira, the officially recognized biography of the Prophet Mohammed :
Ishaq 819 Mohammed had told his commanders to kill only those who resisted; otherwise they were not to bother anyone except for those who had spoken against Mohammed. He then issued death warrants for all of those in Mecca who had resisted Islam. 
Some of them were:
- One of Mohammed’s secretaries. He had said that Mohammed sometimes let him insert better speech when he was recording Mohammed’s Koranic revelations, and this caused the secretary to lose faith.
- Two girls who had sung satires against Mohammed.
- A Muslim tax collector who had become an apostate (left Islam).
- A man who had insulted Mohammed.
- All artists and political figures who had opposed him.
 As a source for hadith we used the websites of University of Southern California,