Apostate prophet defends the oppressed; ostracism against apostates?

In answer to the video "10 Reasons to Reject Islam"

Severing of social ties must be made with apostates who were former hypocrites, especially in the context of war as in the verses that will be quoted, since these former Muslims used to hide their hatred and enmity from other Muslims, and now openly declare it, even striving to make them leave their religion

4:88-89"What is the matter with you, then, that you have become two parties about the hypocrites, while Allah has made them return (to unbelief) for what they have earned?..They desire that you should disbelieve as they have disbelieved, so that you might be (all) alike".

They are therefore to be cut off from the community to avoid the spread of their mischief

4:89"take not from among them friends until they fly (their homes)/hajiru in Allah's way".

Ties with them can only be restored when they decisively return to Islam (as indicated by the clause "fi sabilillah/for Allah's sake") and prove their faith to the rest of the community through difficult sacrifices such as leaving their homes and doing hijra in Allah's way, forsaking the domain of evil for an environment where they can practice their faith without restrictions, as the true believers were doing. If they do not do so then their expression of Islam is only for the purpose of spying and destruction, serving the purpose of those with whom Muslims are at war. In this case

4:89"if they turn back, then seize them and kill them wherever you find them, and take not from among them a friend or a helper".

They must be executed because of their open and secret hostile activities. However if those apostates refuse to flee their homes in Allah's way but nevertheless end the threat from within the community, by migrating for

4:90"a people between whom and you there is an alliance"

or who decide to remain within the Muslim community but have decisively abandoned all hostilities

4:90"who come to you, their hearts shrinking from fighting you or fighting their own people..withdraw from you and do not fight you and offer you peace, then Allah has not given you a way against them".

This Quranic passage establishes the social ruling as regards apostasy. The Quran frames it exclusively in the context of war, which is also the historical context in which the early scholars of Islam discussed the law of apostasy. That is why neither the Quran nor the scholars impose a punishment solely for the act of apostasy, but when it is coupled with hostile activity, verbal or physical. 

Ridda is the word used in reference to those who engage in this multifaceted behavior. This historical perspective is often missed, disregarded or obscured whenever critics quote a saying from the prophet on apostasy, or the rulings of the fuqaha'. One can now understand the words of the prophet 

"The one who leaves his religion AND SEPERATES from the community, kill him". 

Here, the apostate is to be killed if he in addition severes all ties with the community. In those days, this amounted to joining enemy ranks. If the apostate remains in the community he is left unharmed. We thus see the prophetic practice in clear congruence with the aforementioned Quranic passage.

To further corroborate, under Uthman's caliphate, a man named Abdullah Ibn Saba and his followers deeply resented Uthman, favoring Ali instead whom they saw as a semi divine figure more eligible to be caliph. Their over exaltation of Ali took them outside the fold of Islam, making them apostates. Their true aim by feinting conversion was to spread political and social discord to destabilize the caliphate. They planned on capturing and killing Uthman should he refuse stepping down, and Uthman was eventually murdered. Ali eventually arrested them, exiled some of them and executed others. The fact some were exiled shows that although they were all considered apostates, they did not all qualify for the death penalty. The executions were not motivated by choice of creed, which isnt an endorsed practice by the Quran, but rather for the capital offense of fasad fil ard, which per the Quran warrants the death penalty. Although the brief and most authentic reports do not clearly say how this was done, some say that they were first burned then thrown into a ditch while others say they were first beheaded then had their lifeless bodies burnt. 

In both possible cases, Ali had done something which the prophet forbade;

- the first potential misdeed was execution by fire. It is reported "When we intended to depart, Allah's Apostle said,

"I have ordered you to burn so-and-so and so-and-so, and it is none but Allah Who punishes with fire, so, if you find them, kill them".

In another report

"We were with the Prophet and we passed by a colony of ants which had been burned, and the Prophet became angry and said, ‘It is not fitting for any man to punish with the punishment of Allah.” 

- the second potential misdeed was mutilation of lifeless bodies. It is reported

"The Prophet forbade robbery (taking away what belongs to others without their permission), and also forbade mutilation (or maiming) of bodies.”

The traditions explain that this instruction is rooted in a Quranic verse

16:126"And if you take your turn, then retaliate with the like of that with which you were afflicted; but if you are patient, it will certainly be best for those who are patient".

This verse is said to have been revealed after the prophet had seen the violent manner in which his uncle Hamza's dead body had been ripped open and then threatened

"Never yet have i felt more anger than now i feel; and when next time God gives me victory over Quraysh, i will mutilate thirty of their dead".

This emotional, on the spot declaration was never fulfilled, and the prophet in addition forbade mutilation as shown above, in obedience to the Quranic directive. Even in warfare, killing must be swift, without recourse to inefficient weapons that cause unnecessary suffering 

"The Prophet forbade the throwing of stones (with the thumb and the index or middle finger), and said "It neither hunts a game nor kills (or hurts) an enemy, but it gouges out an eye or breaks a tooth".

When ibn Abbas learned of what Ali had done (either burning or mutilating), he publicly rebuked him by appealing to the prophetic sunna mentioned above, which embarrassed Ali, hence his first reaction

"Wayh Ibn Abbas!".

Ali either knew about the prophet's commands but let his emotions overcome him in the execution of the right course, or had forgotten them. So he admitted his error and praised ibn Abbas for speaking the truth

"When ‘Ali was informed about it he said: How truly ibn Abbas said!"