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NationalSocialist Thank you for asking me questions about my faith. Yes, I'm in love with the Quran because it speaks to my heart and my mind and it's a revelation from my Creator. I study the Quran daily and I'd be glad to discuss those verses with you.
The first verse you shared [3:28] has a translation error. The proper translation of it is as follows:
[Quran 3:28]
The believers should not make the disbelievers their allies rather than other believers– anyone who does such a thing will isolate himself completely from Allah– except when you need to protect yourselves from them. Allah warns you to beware of Him: the Final Return is to Allah.
There's a difference between the word Friends and Allies. In Arabic, friends means (أصدقاء: asdiqa), while allies means (أَوْلِيَاءَ: awlia). The Arabic text of this verse is the following:
لَا يَتَّخِذِ الْمُؤْمِنُونَ الْكَافِرِينَ أَوْلِيَاءَ مِنْ دُونِ الْمُؤْمِنِينَ وَمَنْ يَفْعَلْ ذَلِكَ فَلَيْسَ مِنَ اللَّهِ فِي شَيْءٍ إِلَّا أَنْ تَتَّقُوا مِنْهُمْ تُقَاةً وَيُحَذِّرُكُمُ اللَّهُ نَفْسَهُ وَإِلَى اللَّهِ الْمَصِيرُ
Now, what is the difference between Friends and Allies?
Friends: Is a social term, which means a person with whom one has a bond of mutual affection.
Allies: Is a political term, which means a state formally cooperating with another for a military or other purpose.
This verse is political, it's talking to Muslim leaders. In politics, there are countries who are allies to one another for different purposes, either for protection or mutual benefits.
Allah doesn't forbid Muslims from having friendships or good relationships with people of different faiths. In fact, the prophet, peace be upon him, had Jewish neighbors, and he used to visit them and have meals with them.
[Quran 60:7-9]
Allah may still bring about affection between you and your present enemies– Allah is all powerful, Allah is most forgiving and merciful– and He does not forbid you to deal kindly and justly with anyone who has not fought you for your faith or driven you out of your homes: Allah loves the just. But Allah forbids you to take as allies those who have fought against you for your faith, driven you out of your homes, and helped others to drive you out: any of you who take them as allies will truly be wrongdoers.
The second verse is clearly talks about Muslims in state of war. Here's the verse and its context:
[Quran 4:84-85]
So [Prophet] fight in Allah’s way. You are accountable only for yourself. Urge the believers on. Allah may well curb the power of the disbelievers, for He is stronger in might and more terrible in punishment. Whoever speaks for a good cause will share in its benefits and whoever speaks for a bad cause will share in its burden: Allah controls everything. But [even in battle] when you [believers] are offered a greeting, respond with a better one, or at least return it: Allah keeps account of everything.
It's normal, in the battle field, a fighter has to be aggressive to defend his cause. But even in battle field, Allah commands Muslims to seek peace if their enemies seek peace, and you can find this principle throughout the Quran.
You will never find a verse in the Quran that commands killing civilians or innocent people. Even in war, the prophet Muhammad, peace be upon him, commanded Muslims to never kill women, children, elders, unarmed men, men of religion such as rabies and priests. Also, Muslims are not allowed to attack people inside their homes, or even to cut trees. These are the principles of Islam in state of war. How about when they are in state of peace? Think about it.