Apostate prophet has a wild card; didnt Muhammad order assassinations?

In answer to the video "The Most Violent and Awkward Quran Verse"

Even when he permitted the killing of Thumama b. Uthal, the chief of Banu Haneefa who had assassinated a number of the Prophet’s Companions, and had even plotted to kill the Prophet himself, yet when he was captured, not only was he given to drink from the prophet's own she-camel but after repeated invitation to Islam and repeated rejection, was eventually set free. He returned to the prophet's mosque and eventually converted, impressed like many others by the prophet and Islam's high morality. He knew he deserved the death penalty, as seen from his own answer

"If you do me a favour, you will do a favour to a grateful person. If you kill me, you will kill a person who has spilt blood. If you want wealth ask and you will get what you will demand"

yet the prophet neither was vengeful, nor wanted favors and much less money from him, despite his influential tribal position. Upon his arrival to Mecca and after an enthusiastic declaration of faith, in his zeal he implicitly answered a questioner that he had always been a Muslim

"When he reached Mecca, somebody said to him: Have you changed your religion? He said: No! I have rather embraced Islam with the Messenger of Allah (may peace be upon him)".

The prophet had to temper Thumama's overzealousness later on; when he returned to his tribe and the most influential among the people of Yamama converted after hearing his story. Thumama convinced them to halt all grain supply to the Quraysh. Such a sanction would have been highly effective in draining the Quraysh, but the noble prophet interceded on behalf of those very ones that had starved him and his early companions in a ravine, persuading the people of Yamama to resume trading with Quraysh, preferring to take the harder but nobler route to victory than the faster one at any cost

"The Messenger of Allah (Sallalahu Alayhi Was-Sallam) did not have to choose between two matters, but that he chose the easier of them as long as it was not a wrong action. If it was a wrong action, he was the furthest of people from it".

There are other similar instances of the prophet catching a person red handed trying to murder him, even while easily having power and right to exact revenge, but instead chose forgiveness. It was the case with Fadala b. ‘Umayr after the conquest of Mecca where he had full dominion over the people. I was also the case before, with the Bedouin man (al-Ghawrath b. al-Harith) that sneaked to him while he was asleep following a military expedition. The prophet woke up while he was about to unsheeth his sword and kill him, but calmly reasonned with him at that point and let him go free.

After unmasking the Jewess Zaynab b. al-Harith that had given him a poisonned lamb to eat, he refused to kill her and even forgave her. 

On his return by night from the expedition of Tabuk and as he was riding his camel on a route passing above a ravine, a group of camel riders came fast in his direction in an attempt to scare his own camel that he might fall into the ravine. The prophet however sensed their intentions and preemptively gestured so as to scare the coming camels and signify to the men that he uncovered their plan. They consequently quickly retreated. Even though the prophet's companions identified the perpetrators, the prophet isntructed them not to denounce them because

"it was possible that they might repent". 

His tolerance, patience and forbearance were indiscriminate and touched people from all social spheres

“Do not be mere imitators, treating well only those who treat you well and doing wrong to those who do you wrong. Instead, accustom yourselves to do good if people do good and not to do wrong if they do evil”  Aisha said "The Messenger of Allah did not take revenge for anything against himself, but if the sacred law of Allah was violated then he would take retribution for the sake of Allah".

This attitude of the prophet, his forbearance was a pattern which remained throughout his 23 years of prophethood, whether at the best or worst moments the community went through. For instance following the defeat at Uhud due to some of the troops breaking up against the prophet's orders, allured by the spoils left behind by the retreating pagan army. The victory was on the Muslim side up to that point, after which the opponents took the upper hand. Even in such situations, where the lack of discipline of some, brought death and defeat on the nascent community, the prophet did not behave as would have been expected from a field commander and nation leader. He did not judge, condemn or punish the guilty and deserters.

3:159-161"And it was by Allah’s grace that you dealt gently with your adherents, for if you had been harsh and hard of heart, they would indeed have broken away from you. Pardon them, then, and pray that they be forgiven. And take counsel with them in all matters of public concern; then, when you have decided upon a course of action, place your trust in Allah, for, of certainty, Allah loves those who place their trust in Him. If Allah supports you, none can ever overcome you; but if He should forsake you, who could support you thenceforth? In Allah, then, let the committed Muslims place their trust. And it is not conceivable that a prophet should deceive [in military affairs or in anything else], since he who deceives shall be faced with his deceit on the Day of Resur- rection, when every human being shall be repaid in full for whatever he has done, and none shall be wronged [by any injustice]".

Despite the unsettling situation, he remained a tranquil and friendly administrator, fully involved into improving the society he belonged to. He acknowledged the deficiencies of human nature especially in times of war. At that moment it the prophet had to have a clear mind to understand the individual circumstances that led these first-time offenders to do what they did. He had to think with his heart, not to react in proportion to the adversity that resulted from their lethal mistakes

9:128"Indeed, there has come unto you an Apostle from within yourselves: heavily weighs upon him [the thought] that you might suffer [in the life to come], full of concern for you [is he, and] full of compassion and mercy toward the committed Muslims".