That's a selective reading. The quran leaves plenty of room to allow governments to punish apostates, and in some places, clearly condones it. And even if that weren't true, it is pointless to say that islam itself allows freedom of consience, when most islamic countries today and most islamic societies throughout the ages have had laws against apostacy, often with harsh punishments including death.Quran is more clear about shirk/idolatry. As for apostacy -- Quran mentions freedom of conscience as one of its basic tenets. "There is no compulsion in religion (2:256)," and "Let him who will believe and let him who will disbelieve (18:29)." Belief is mentioned as a matter of personal choice. The next part of the latter verse makes it clear that God - not man - is the sole judge of faith (or the lack thereof) and will reward or punish as He wills in the Hereafter.
BTW, from the hadiths:
Ali burnt some people and this news reached Ibn 'Abbas, who said, "Had I been in his place I would not have burnt them, as the Prophet said, 'Don't punish (anybody) with Allah's Punishment.' No doubt, I would have killed them, for the Prophet said, 'If somebody (a Muslim) discards his religion, kill him.'
A man embraced Islam and then reverted back to Judaism. Mu'adh bin Jabal came and saw the man with Abu Musa. Mu'adh asked, "What is wrong with this (man)?" Abu Musa replied, "He embraced Islam and then reverted back to Judaism." Mu'adh said, "I will not sit down unless you kill him (as it is) the verdict of Allah and His Apostle.
" 'Abdullah (b. Mas'ūd) reported Allah's Messenger as saying: It is not permissible to take the life of a Muslim who bears testimony (to the fact) that there is no god but Allah, and I am the Messenger of Allah, but in one of the three cases: the married adulterer, a life for a life, and the deserter of his Din (Islam), abandoning the community."]
And this is what sharia has to say:
In Islamic law (sharia), the view among the majority of medieval jurists was that a male apostate must be put to death unless he suffers from a mental disorder or converted under duress, for example, due to an imminent danger of being killed. A female apostate must be either executed, according to Shafi'i, Maliki, and Hanbali schools of Sunni Islamic jurisprudence (fiqh), or imprisoned until she reverts to Islam as advocated by the Sunni Hanafi school and by Shi'a scholars.[55]
This is what hass been practised by muslims since the beginning of islam. So saying that islam allows freedom of consience but muslims don't, doesn't change anything.