Opponents of Islam usually misquote 4:90 in a misleading way by leaving out the words “until they emigrate.” Also, they leave out the very next verse which clarifies the entire point. The verse under question is:
They wish that you should disbelieve as they have disbelieved, so that you may become all alike. Take(Surah an-Nisa’, 4:90-91)
not, therefore, friends from among them, until they emigrate in the way of Allah. And if they turn away, then seize them and kill them wherever you find them; and take no friend nor helper from among them; Except those who are connected with a people between whom and you there is a pact,or those who come to you, while their hearts shrink from fighting you or fighting their own people. And if Allah had so pleased, He would have given them power over you, then they would have surely fought you. So, if they keep aloof from you and fight you not, and make you an offer of peace, then remember that Allah has allowed you no way of aggression against them.
This verse refers to people who “turn away” after “they emigrate.” Emigration is moving from one territory to another territory and changing political alliance. The crime described in this verse is not religious apostasy, the crime is political treason. Treason during warfare is punishable by death.
Also, the very next verse makes it abundantly clear that even those who are described here as turning away from the Muslims are to be given complete peace. No fighting is permitted against them unless they themselves wage war against the Muslims.
Those who believe, then disbelieve, then again believe, then disbelieve, and then increase in disbelief, Allah will never forgive them nor will He guide them to the way.(Surah an-Nisa’, 4:138)
Those who become apostates still have the door of forgiveness open to them in the presence of Allah Almighty, and no human has the right to deprive them of this door of forgiveness by killing them. Not only that, but a person can return to Islam and again become an apostate and still there is no punishment. Only when Allah Almighty, in His perfect knowledge of that person’s heart, knows that he increases in disbelief after becoming a disbeliever the second time, does He condemn that person to spiritual torment, with no worldly punishment being mentioned and no human being given the right to punish
And obey Allah and obey the Messenger, and be on your guard. But if you turn away, then know that on Our Messenger lies only the clear conveyance of the Message.(Surah al-Ma’idah, 5:93)
[O Muhammad], Admonish, therefore, for(Surah al-Ghashiyah, 88:22–25)
youart but an admonisher; You are not a warden over them; But whoever turns away and disbelieves, Allah will punish him with the greatest punishment.
And if thy Lord had enforced His will, surely, all who are on the earth would have believed together. Wilt thou, then, force men to become believers?(Surah Yunus, 10:100)
As for the Bible, it commands concerning apostates:
If your brother, the son of your mother, your son or your daughter, the wife of your bosom, or your friend who is as your own soul, secretly entices you, saying, “Let us go and serve other gods,” which you have not known, neither you nor your fathers, of the gods of the people which are all around you, near to you or far off from you, from one end of the earth to the other end of the earth, you shall not consent to him or listen to him, nor shall your eye pity him, nor shall you spare him or conceal him; but you shall surely kill him; your hand shall be first against him to put him to death, and afterward the hand of all the people. And you shall stone him with stones until he dies, because he sought to entice you away from the Lord your God, who brought you out of the land of Egypt, from the house of bond- age. So all Israel shall hear and fear, and not again do such wickedness as this among you.(Deuteronomy 13:6–11)