Apostate prophet isnt the best prosecutor; executing apostates in Islam?

In answer to the video "The Fate of the Jews of Medina (TGP 1)"

To further corroborate the notion that spiritual apostasy isnt what triggers the death penalty, 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!"

Similarly the misquoted reports about Abu Bakr's ridda wars do not come in the context of apostasy. The people fought against were regarded as Muslims according to many other reports, although a minority had apostised. They were fought for their refusal to pay due government taxes and poor rate, and after they initially and unexpectedly attacked those that sided with Abu Bakr on the issue, and after causing bloodshed among government ranks and attempted to overthrow the first caliph. Prior to giving further details about this event, it is important noting that the Quran sanctions warfare against anyone, including Muslims, who refuse to desist from destructive practices such as riba 2:278-9. The events of the ridda war occured shortly after the prophet's death when many disheartened recent converts apostised and others attempted to reduce their community contributions.

Umar is reported to have pleaded with Abubakr to be more lenient with those that refused paying their dues, which he categorically refused. Clearly the issue was not about spiritual apostasy or else Abubakr would have acceded to Umar's request, accepting that they pay less in exchange of their adherence to the Muslim community. Abubakr sent them an official letter calling them back to Islam, those very people who were nominal Muslims, but that refused adhering to the laws of the Islamic state. He instructed his emissaries to fight the rebels after they have been informed of their obligations towards the state and have rejected

"(the duties) that are incumbent upon them and [the advantages] that accrue to them, and (the emissary) should take what is [imposed] on them and give them what they are due".

In his letter Abubakr additionally appealed to the prophet's practice in a similar situation. When he was confronted to Muslims who rebelled against the state and refused paying their dues, unjustly taking advantage of the system which others were sacrificing their own wealth and lives to maintain

"he struck whoever turned his back to Him (God) until he came to Islam, willingly or grudgingly".

Such a behavior is equal to turning one's back to God, as is represented by the state religion. This isnt speaking of simply renouncing the religion while remaining a full fledged citizen with his rights and obligations.

The rebels of the ridda war launched their assault by night while the majority of the Muslim soldiers were sent on an expedition outside Medina. Abu Bakr fought back with his people and killed those who were involved. It is with such historical and Quranic perspective that the killing of apostates as reported in the history and hadith books should be understood, spiritual apostasy was never the sole charge warranting the death penalty, but rather political apostasy ie socio-political destabilisation and conspiracies to commit bloodshed, especially in times of war or other sort of trials that caused the early Muslims to be on high alert against those who wished to overthrown the system.

In addition, some among the early Muslims' enemies pretended converting in attempts to infiltrate the community and harm it through inciting sedition and providing vital information in times of war 3:72,33:60. All governments would punish and sometimes execute foreign spies, double agents, or traitors to an enemy with whom one is at war. These are the people covered in the saying

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

This clearly puts 2 condition for the execution of an individual in war times, leaving the religion combined with separation from the community to join the enemy. Leaving the religion while remaining a full fledged citizen with his rights and obligations does not warrant the death penalty. This openly declared threat would make the conspirators think twice before engaging in their insidious behavior. All scholars have understood that leaving Islam must be coupled with a will to harm it and its people, to warrant the death penalty. Ibn Taymiyah said

"Muhaarabah (waging war against Islam) is of two types: physical and verbal. Waging war verbally against Islam may be worse than waging war physically – as stated above – hence the Prophet (peace and blessings of Allaah be upon him) used to kill those who waged war against Islam verbally, whilst letting off some of those who waged war against Islam physically. This ruling is to be applied more strictly after the death of the Prophet (peace and blessings of Allaah be upon him). Mischief may be caused by physical action or by words, but the damage caused by words is many times greater than that caused by physical action; and the goodness achieved by words in reforming may be many times greater than that achieved by physical action. It is proven that waging war against Allaah and His Messenger (peace and blessings of Allaah be upon him) verbally is worse and the efforts on earth to undermine religion by verbal means is more effective".