Couldn't it be that they accepted his teachings but not his absolute(?) leadership?
Actually, it couldn't be that.
Muhammad had a progressive series of revelations rather than all at once, and many of them happened AFTER their later conversions. In short, you can't really have been a Muslim and at the time not have accepted his leadership.
Why does it mean that it ignores the polytheistic tradition of Arabia?
Because it ignores the cultural issues which led to the conflict with Islam. The Quraysh may often be depicted as money obsessed but at the very least they tend to still be shown as quite devout to their polytheistic ways. Islam leaving no room for the ideals of the Quraysh as well as its views regarding preisthood were radical enough to be a uniting factor for Arabs and do not make as much sense otherwise.
And you should remember that the Quran is an unreliable source written down decades after the events. And if most historian have a problem with the traditional sources about the Islamic expansion when we should ask ourselves if the Quran is as reliable source or if it is pure propaganda like the Christian Gospels (which are unreliable because several events mentioned there never happened)?
Firstly, this is further compounding the idea that you don't know much on the topic... I know that may sound rude, but the Quran isn't a documentation of the life of Muhammad or the conflict with the Quraysh. Now there are chapters which describe behaviour DURING those moments, but they are both A) minimal and B) few. To the extent that history is in the Quran it is largely "here is a battle that happened to us, here is what we can learn from it".
The history of Muhammad and his life largely comes through a collection of writings called the Hadith rather than the Quran. The Hadith and the examining of them for historical accuracy is actually a big theme in Islamic scholarship. One such often rejected one is where the 72 Virgins idea comes from. You are right in that there is real concern as to historical accuracy in Islam, but the matter of religion regarding the Quraysh really isn't one of them.
What does that mean? It means that it must be possible to research the origins of Islam without fixed expectations even if the results may not be the ones you've hoped to find. It must be possible to ask certain questions. It must be possible to question the oral tradition of Islam. But this does not happen because of fear. Every scholar of Islam studies or the history of early Islam fears not only religious fundamentalists but also the Islamic scholars. And those fear that if such scientific research does not deliver the expected results it will harm Islam. It seems that the leaders (religious and political) do not have any faith in the Muslims and that they fear that unexpected results may be the end of Islam. It seems that they believe that any scientific research without fixed expectations will come to the conclusion that the Quran is one big lie (as if religion has anything to do with history)...
I have got a feeling that you are on a bit of an anti-religious bent here... I am an atheist too (for I presume you are one based on the last section) but I am actually here for discussion. Blanket statements such as "It must be possible to question the oral tradition of Islam" and "Every scholar of Islam studies or the history of early Islam fears not only religious fundamentalists but also the Islamic Scholars" don't actually help convince people of your point regarding the Quraysh as it doesn't offer anything in turn. In case that sounds like I am being mean, perhaps this example will help you understand why such a tirade does not help the discussion with an example.
Al Qaeda is bad. In that statement, nothing is provided that actually tells you anything about early Islam. It is merely a disaproval of a group rather than an actual fruitful discussion of the history of early Islam.
I am more than happy to continue this discussion, but please keep it on topic.