We shall look at some of those verses.
"Those who disbelieve after their belief and then sink more and more into disbelief, their repentance will never be accepted and they are the ones who have gone astray. "Those who disbelieve and die while they (still) are unbelievers, (even) the earth full of gold shall not be accepted from them if they (try to) offer it in compensation. They shall have a painful chastisement and they shall have no helpers."23
When one studies the context and the occasion when this passage was revealed, it becomes clear that these verses were about some former idol-worshippers or Ahlul Kitab who had become Muslim, and later on they renounced Islam and fled to Mecca. Some of them (e.g., al-Harith bin Suwayd bin as-Samit) regretted their apostasy and asked for forgiveness. They were forgiven, and they were allowed to return back to Medina.24
As you see, these verses were revealed about the case of one or more murtad milli who had fled from the control of Muslims. As we have explained above, in case of murtad milli, he is given the chance to repent; and if he repents, then he is not to be killed. This example actually proves that shar`iah law is in accordance with the holy Qur'an.
A murtad milli who does not repent may flee from the control of the Muslims, but, as the last verse says, he can never flee from the curse of Allah, the angels and all men together in this world as well as the hereafter.
This verse is talking about the chastisement of murtad in the hereafter. It does not automatically follow that there is no punishment for them in this world. Affirmation of one does not automatically deny the other. For example, if verse 4:93 says "Whoever kills a believer intentionally, his punishment is hell, in it he shall dwell forever. Allah will send His wrath on him, curse him and prepare a painful chastisement for him" -- this does not mean that there is no worldly punishment for a murderer. The worldly punishment for murder could be found in other verses of the Qur'an or the sunna.
Firstly, these two verses were revealed with the verses before them in connection with the Battle of Uhud. The verses refer to the idol-worshippers and infidels of Mecca who had come to fight the Muslims; it has no connection with apostasy. Probably the brother looked at the words in N.J. Dawood's translation "quickly renounce their faith" and assumed that it refers to Muslims becoming kafirs. No, not at all.
Secondly, the brother has deduced from this verse that "the apostates should live". This is also an incorrect understanding. "God intends to give them no share in the Hereafter" does not mean that Allah desires that such people should live longer in this world. It just means that their prolonged life should not be taken as an indicator by them that they are okay in the eyes of Allah. This concept is further clarified in the next verse:
"The unbelievers should not think that We are granting them respite for their own good, rather We grant them respite so that they may (eventually) increase in sins and (accordingly) they shall have a disgraceful chastisement." (3:178)
For example, Saddam should be killed by anyone who has the opportunity to do so; but, if he escapes punishment at the hands of the believers, then he should not think that God is on his side--no; the more he lives, the more his sins will increase, and he will deserve even more chastisement in the hereafter.25 So "giving respite" does not mean suspending the punishment or leaving the judgment to the hereafter.
But if they turn back (from belief and migration), then seize them and kill them wherever you find them, and do not take from them any as a friend or a helper. (Seize and kill such people) except those (among them) who reach a tribe with whom you are joined in an alliance, or who come to you with hearts constricted from fighting you or fighting their own people...Therefore if they withdraw from you and do not fight you and (instead) offer you peace, then (know that) Allah has not given you permission (to fight) against them. (4:89-90)
First of all, these verses are about the polytheists of Mecca in general--the kuffar as well as those who became murtad. They do not talk about individuals and their punishment.
Secondly, even if we concentrate on the Meccans who had come to Medina, accepted Islam as their faith, and then returned back to Mecca and became kafir--we see that this is the case of murtad milli. And the verses clearly state that if they return back to Islam, then you can take them as friends. But if they do not return to Islam, then "seize them and kill them wherever you find them".
Thirdly, later part of the passage talks about a situation where such groups or individuals form an alliance with tribes (or countries) with whom you also have a peace treaty, then that peace agreement would now cover them also; and, therefore, you should not do anything to them. This is seen in the views of the jurists who say that if a murtad flees from daru 'l-Islam, then it is not obligatory to pursue him and kill him.26
These are just some examples of how to study the Qur'anic verses: in their proper historical context and not just in isolation. Other similar verses can be understood in the same light.
23. The translation of the Qur'anic verses is my own.
24. See Majma`u 'l-Bayan of at-Tabrasi (a Shi`ah commentary) and ad-Durru 'l-Manthur of as-Suyuti (a Sunni commentary).
25. This was written in 1998; presently Baghdad's Butcher is in prison and on trial.
26. See note no. 6.