There are three groups of polytheists mentioned in chapter 9, verses 1-15. They are:
(i) A group fought wars against Muslims, and then made a peace treaty with Muslims, and then violated the peace treaty. God talks about this group in verses 1, 2, 3, 5, 6, 13, 14 & 15.
(ii) A group fought wars against Muslims, and then made a peace treaty with Muslims, and did not violate the peace treaty. God talks about this group in verses 4 & 12.
(iii) A group that did not fight war against Muslims nor support Muslims in public. Instead they kept quit. God talks about this group in verses 7, 8, 9, 10 & 11.
God tells Muslims how to treat the first group of polytheists:
• God says he and his messenger canceled the peace treaty between Muslims & polytheists (See 9:1) because polytheists broke the peace treaty by attacking Muslims in the sacred months and deciding to expel the Messenger of God (See 9:13).
• Muslims are not allowed to fight in the sacred months. So, God tells Muslims to wait till the sacred months are over to answer the violation of peace treaty by polytheists. When sacred months are over, God tells Muslims to attack polytheists, kill them, and capture them (See 9:5).
• In addition, God tells Muslims not to harm 2 groups of polytheists during the war. The first group is who accept Islam (See 9:5). The second group is who seek protection and agree to hear the recitation of Quran in return for their protection. God tells Muslims to let the polytheists go free after the war who sought protection in exchange for hearing the recitation of Quran (See 9:6).
God tells Muslims how to treat the second group of polytheists:
• God tells Muslims to fulfill the peace treaty with polytheists because they did not violate the peace treaty so far (See 9:4).
• God tells Muslims that they do not have to bind themselves to the peace treaty if polytheists break the peace treaty in future. God tells Muslims to force polytheists to stop their aggression against Muslims if they violate the peace treaty (See 9:12).
God tells Muslims how to treat the third group of polytheists:
• God tells Muslims to be upright toward the polytheists as long as polytheists are upright toward Muslims (See 9:7).
• God tells Muslims to be careful about the polytheists because polytheists use their sweet talk and kinship to misguide Muslims. God says the hearts of the polytheists are against Muslims and they actually don't care about the kinship with Muslims. God says they will not hesitate to harm Muslims when they get a chance (See 9:8-10).
• God tells Muslims not to take polytheists as their brothers despite of their kinship with polytheists. God says the only time Muslims can take polytheists as their brothers if polytheists become Muslims (See 9:11).
In conclusion, God only orders to kill and capture a group of polytheists (not all polytheists) who fought war against Muslims, and then made a peace treaty with Muslims, and then violated the peace treaty by attacking Muslims. There is nothing wrong with killing and capturing your enemies in the battlefield for self defense.
References:
9:1- This is a declaration of cancellation of peace treaty from God and his Messenger, to those with whom you had made a peace treaty among the polytheists.
9:2- So travel freely, [O polytheists], throughout the land [during] four months but know that you cannot cause failure to God and that God will disgrace the disbelievers.
9:3- And [it is] an announcement from God and His Messenger to pilgrims that God and his Messenger is free from obligation to the polytheists. So if you [polytheists] repent, that is best for you; but if you turn away - then know that you will not cause failure to God. And give tidings to those who disbelieve of a painful punishment.
9:4- Except those of the polytheists with whom you made a treaty and have not broken the treaty with you in anything or supported anyone against you. So, fulfil the peace treaty with them. Indeed, God loves the righteous.
9:5- And when the sacred months have passed [when four months are over], kill the polytheists wherever you find them and capture them and besiege them and sit in wait for them at every place of ambush. But if they repent, establish prayer, and give obligatory alms [become Muslims], leave them alone. Indeed, God is Forgiving and Merciful.
9:6- And if any one of the polytheists seeks your protection, then grant him protection so that he may hear the words of God. Then escort him to where he can be secure. That is because they are a people who do not know.
9:7- You do not have any peace treaty with polytheists except those polytheists with whom you made a treaty near the Sacred Mosque. So as long as they [polytheists] are upright toward you, be upright toward them. Indeed, God loves the righteous.
9:8- You do not have peace treaty with polytheists with whom you did not make a treaty near the Sacred Mosque. If polytheists prevail against you, they will not respect neither the blood relation you have with them nor the promise of protecting each other. Their lips are on your side but their hearts are against you. Most of them are wrongdoers.
9:9- They [polytheists] have exchanged the signs of God and averted [people] from His way for their personal gain. Indeed they are evildoers.
9:10- They [polytheists] do not respect their family ties with the believers nor promises of protection. They are transgressors.
9:11- But they [polytheists] repent, establish prayer, and give obligatory alms [become Muslims], they would be your brothers in the religion. We explain Our revelations to people of knowledge.
9:12- Fight against the leaders of the polytheists if they violate their established peace treaty with you and revile your faith. Force them to stop their aggression against you. You do not have to bind yourselves to the treaty if they violate it.
9:13- Would you not fight a people who broke their peace treaty with you and determined to expel the Messenger, and they had begun [the attack upon] you the first time? Do you fear them? But God has more right that you should fear Him, if you are [truly] believers.
9:14- Fight them. May God punish them by your hands, humiliate them, give you victory over them, and delight the hearts of the believers.
9:15-and appease their anger. God accepts repentance from whomever He wants and He is All-knowing and All-wise.
