What does killing of the polytheists according to the 5th verse of Tevbe Surah mean?

One of the verse in Quran that the atheists criticize and show it as a reason to their denial is the 5^th verse of Tevbe Surah. They get the term ‘’kill the polytheists wherever you find’’mentioned here and claim that Islam is a religion of “savageness and war“. In fact the first part of Tevbe Surah were the polytheists are mentioned is the highest peak of toleration.Let us define the words

“Shirk“ and “Mushrik“ before we start the subject. Shirk does not only mean worshipping icons. Anything favoured more than Allah or his consent is considered to be Shirk. The person who behaves so is called Mushrik. Since the Mushrik people in the era of our prophet were against the spread of Islam, they outraged the Muslims. Everybody who watched the movie called “Cagri – Epistle“ can view this era easily in his mind. Our prophet and the people who believed in him immigrated to Madinah because of this outrage. The immigrants (Muhajirun) and the people of Madinah who helped them (Ensar) got along well in a short time. The first constitution in the Islamic history was prepared here and the Madinah State was established. The relations, responsibilities and obligations of the Muslim who considered Quran as their constitution between those who followed other rules were assured by the rules known as The Madinah Constitution in history. Later on many agreements were made with the neighbouring polytheist tribes and other tribes in Saudi Arabia. One of these agreements is the Hudeybiye Agreement.

According to the Hudeybiye Agreement the Muslim and the polytheists were not going to fight for 10 years and both parties were not going to attack each other in any way. But some of the polytheists breached this agreement and attacked the Muslims in the second year of the agreement. Upon this, our prophet conquered Makkah. But he did not attack the polytheists meanwhile. Allah gave a period of 4 months (Haram Months) to the polytheists to leave Makkah and/or swear to give up their attacks. If they do not regret their attacks to the Muslims within this period or not leave Makkah, they were supposed to be killed wherever found. But in the 4^th verse it ordered not to attack those obey the agreement and do not help the people who attack Muslims. They were set apart.

Thisis a certain warning from Allan and his prophet to those polytheists with who you signed an agreement. (Tevbe Surah 1)

From now on you have four months to go free on this earth. Do not forget that you cannot incapacitate Allah. Allah really humiliates the polytheists.  (Tevbe Surah 2)

…It is better for you to swear to give up; if you do not, do not forget that you cannot incapacitate Allah. Tell the polytheists that a torment is waiting for them. (Tevbe Surah 3)

But the polytheists who obey the agreement signed with you and those who do not help your enemies are excluded; complete the agreement until the end of its period. Allah favours the obedient. (Tevbe Surah 4)

When the period of four months is completed kill the polytheists wherever you find them, arrest them, surround them and close any possible way available for them. If they swear to give up and pray and practice charity, open their ways. Allah is a real forgiver. (Tevbe Surah 5)

After the end of the period Muslims were entitled to kill the polytheists who attacked them and killed their beloved ones. But there is a very important warning in the 6^th verse. If those polytheists who kill you beloved ones ask for forgiveness and sear to give up, you should forgive them.

If any of the polytheists, ask your forgiveness, forgive him; so you will be fulfilled Allah’s order, then take them to a safe place.This is because they are an ignorant society. (Tevbe Suresi 6)

I ask those people who consider this verse as savageness: What would you do if someone rapes your wife and sister and kills your son? Would you tell him to kill his parents waiting inside too? Of course no. You come against that person with all your means and protect your beloved ones.

I am asking again: If those people who savage your beloved ones ask for forgiveness, would you forgive them? I do not think so. Accordingly you do not have the right of questioning the tolerance in Islam.