Islam critiqued almost admits; no death for apostasy. What about specific controversial incidents?

In answer to the video "The Logic of Muhammad"

Here is an example to 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!"