Just go read historical books on the subject. For the early Islamic conquests there are a lot of non-biased books.

If the only form of different treatment is regarding administrative military positions I really don't personally see the issue, the same way I would understand why a Christianity state would want one of their own believers to be at a higher administrative position

The Ming and Qing dynasties both employed Muslim commanders of several of their armies. If they were as intolerant as their contemporary Muslim states, then they wouldn't have done so.

The best example of Muslims are their prophets. If we look at the Middle East it's very corrupt and the reasoning is supposedly 'Islam', but Islam doesn't actually teach half the stuff they do (such as Saudi prohibiting women from driving). If we read the Quran we can see what a Muslim is and isn't allowed to do - we shouldn't use people that just claim this Religion for an example, we should use their source and come to our own discoveries.

The Quran states that believers should go around killing polytheists, that Christians are more valued as friends than Jews, that a woman is worth half a man, and other disturbing content. Muslims, such as Isis, who follow the Quran are part of the problem.