I've seen Anti-Islamic sites quote this verse:
وَدُّوا لَوْ تَكْفُرُونَ كَمَا كَفَرُوا فَتَكُونُونَ سَوَاءً ۖ فَلَا تَتَّخِذُوا مِنْهُمْ أَوْلِيَاءَ حَتَّىٰ يُهَاجِرُوا فِي سَبِيلِ اللَّهِ ۚ فَإِنْ تَوَلَّوْا فَخُذُوهُمْ وَاقْتُلُوهُمْ حَيْثُ وَجَدْتُمُوهُمْ ۖ وَلَا تَتَّخِذُوا مِنْهُمْ وَلِيًّا وَلَا نَصِيرًا {89}
[Shakir 4:89] They desire that you should disbelieve as they have disbelieved, so that you might be (all) alike; therefore take not from among them friends until they fly (their homes) in Allah's way; but if they turn back, then seize them and kill them wherever you find them, and take not from among them a friend or a helper.
This verse seems to be clear that you should kill those whom renegade from Islam. But what they fail to show is the next verse that shows the opposite:
إِلَّا الَّذِينَ يَصِلُونَ إِلَىٰ قَوْمٍ بَيْنَكُمْ وَبَيْنَهُمْ مِيثَاقٌ أَوْ جَاءُوكُمْ حَصِرَتْ صُدُورُهُمْ أَنْ يُقَاتِلُوكُمْ أَوْ يُقَاتِلُوا قَوْمَهُمْ ۚ وَلَوْ شَاءَ اللَّهُ لَسَلَّطَهُمْ عَلَيْكُمْ فَلَقَاتَلُوكُمْ ۚ فَإِنِ اعْتَزَلُوكُمْ فَلَمْ يُقَاتِلُوكُمْ وَأَلْقَوْا إِلَيْكُمُ السَّلَمَ فَمَا جَعَلَ اللَّهُ لَكُمْ عَلَيْهِمْ سَبِيلًا {90}
[Shakir 4:90] Except those who reach a people between whom and you there is an alliance, or who come to you, their hearts shrinking from fighting you or fighting their own people; and if Allah had pleased, He would have given them power over you, so that they should have certainly fought you; therefore if they withdraw from you and do not fight you and offer you peace, then Allah has not given you a way against them.
As you can see, it's clear that if they left Islam, and offerred them peace and didn't fight, they weren't allowed to kill them.
Then why does apostacy rule exist when it's this clear in Quran? Same reason stoning exists when Quran has lashing. It's because hadiths are valued over Quran, contrary to claim of Muslims that hadiths are to be evaluated by Quran.
وَدُّوا لَوْ تَكْفُرُونَ كَمَا كَفَرُوا فَتَكُونُونَ سَوَاءً ۖ فَلَا تَتَّخِذُوا مِنْهُمْ أَوْلِيَاءَ حَتَّىٰ يُهَاجِرُوا فِي سَبِيلِ اللَّهِ ۚ فَإِنْ تَوَلَّوْا فَخُذُوهُمْ وَاقْتُلُوهُمْ حَيْثُ وَجَدْتُمُوهُمْ ۖ وَلَا تَتَّخِذُوا مِنْهُمْ وَلِيًّا وَلَا نَصِيرًا {89}
[Shakir 4:89] They desire that you should disbelieve as they have disbelieved, so that you might be (all) alike; therefore take not from among them friends until they fly (their homes) in Allah's way; but if they turn back, then seize them and kill them wherever you find them, and take not from among them a friend or a helper.
This verse seems to be clear that you should kill those whom renegade from Islam. But what they fail to show is the next verse that shows the opposite:
إِلَّا الَّذِينَ يَصِلُونَ إِلَىٰ قَوْمٍ بَيْنَكُمْ وَبَيْنَهُمْ مِيثَاقٌ أَوْ جَاءُوكُمْ حَصِرَتْ صُدُورُهُمْ أَنْ يُقَاتِلُوكُمْ أَوْ يُقَاتِلُوا قَوْمَهُمْ ۚ وَلَوْ شَاءَ اللَّهُ لَسَلَّطَهُمْ عَلَيْكُمْ فَلَقَاتَلُوكُمْ ۚ فَإِنِ اعْتَزَلُوكُمْ فَلَمْ يُقَاتِلُوكُمْ وَأَلْقَوْا إِلَيْكُمُ السَّلَمَ فَمَا جَعَلَ اللَّهُ لَكُمْ عَلَيْهِمْ سَبِيلًا {90}
[Shakir 4:90] Except those who reach a people between whom and you there is an alliance, or who come to you, their hearts shrinking from fighting you or fighting their own people; and if Allah had pleased, He would have given them power over you, so that they should have certainly fought you; therefore if they withdraw from you and do not fight you and offer you peace, then Allah has not given you a way against them.
As you can see, it's clear that if they left Islam, and offerred them peace and didn't fight, they weren't allowed to kill them.
Then why does apostacy rule exist when it's this clear in Quran? Same reason stoning exists when Quran has lashing. It's because hadiths are valued over Quran, contrary to claim of Muslims that hadiths are to be evaluated by Quran.