I would imagine that the last two-thousand or so years of magical history would probably shake out to some thing like:
For the majority of their history mages would have been either a part of the various religious orders, performing small feats of religious 'miracles' and ritual/runic magics, or they would have been wholly ignorant of their own magic, only finding out about it in the performance of super-human feats in battle. I could probably imagine the Roman Empire being the first place where magic using wands began to be practiced and systematized for the religious elites of society, and with the eventual fall of the Western part of the Empire, the mages would likely have separated themselves from the degradation of muggle society into barbarism. This would, of course, leave a lot of muggleborn mages high and dry, causing them to either enter religious orders or end up dead over the next dozen centuries or so.
Personally, I've always imagined that Merlin was likely a genius spell inventor with a personal quest to reunite the magical and muggle worlds, ala the Roman Empire, with King Aurthur; and likely the one who taught the four founders of Hogwarts, given their own penchant for trying to incorporate the two worlds, albeit on a smaller and less political scale. However good their intentions were in trying to reunite the worlds, the vast majority of mages would have been content to ignore those people who didn't grow up in the magic-only society, with only a few radicals trying to carry on the work of Merlin and the founders in the following centuries. Thus, there would have been very few muggleborns wandering about society, and would have likely been regarded as something of a freak show for disgusted-yet-intrigued purebloods.
What would shake-up the status quo and cause the mages to, however grudgingly, open their society up to muggleborns, would likely be two pretty big things. The first would be the role that muggleborn mages of the Catholic and Protestant Churches would have played in the conquest and subjugation of other mages as the European empires expanded around the world from about 1500 onwards. However, this alone would probably not be enough for the lazy mages to so fundamentally change their society into taking a more open stance. Thus the second reason would have to come from a realization of the dangers inherent in leaving muggleborn mages in the hands of muggles, and I believe that the French Revolution would provide just such an example. Napoleon, employing vast numbers of devoted muggleborns to find and bring the continental magical enclaves to heel, would pretty much force European mages to come to an international accord that would prevent any man from ever using mages in such a fashion again. You could even imagine that they would have him painted as the first and only muggle dark lord.
At any rate, the international accord on the integration of muggleborns into mage society, and then said society being kept a secret from the muggles, would likely keep the European mages quite busy for the next century: training up muggleborns and sending them out as cannon fodder to bring what's left of the world's magical societies under the purview of the Statute of Secrecy. This would probably create a situation where the the purebloods of Europe could justify the muggleborn presence, so long as they weren't mucking about in Europe - and with few job opportunities for the muggleborns except as colonial administrators and soldiers, they wouldn't have stuck around enough to really register as a threat to the purebloods, but rather as a convenient tool to prevent another 'Napoleon' from rising.
However, big changes would come in the 20th century with the increasing prevalence of muggleborns remaining in Europe as the foreign positions came to be filled more by the foreigners themselves, not to mention the explosion in population worldwide causing an equal increase in the birth of muggleborns. The loss of the escape valve that the colonies presented for muggleborns, would have served to radicalize scores of pureblood mages, who would view their traditional society as coming under siege by an ever-increasing number of these 'outsiders'. Grindewald and Voldemort could both be considered symptoms of this problem, but the fact that they mainly employed purebloods to serve as their footsoldiers would have caused the smaller-in-number purebloods to suffer much greater losses in comparison to the ever-increasing muggleborn population; which would again explain why Voldemorts followers were fewer, and could be considered much more radicalized than Grindewald's group.
By the twenty-first century, magical enclaves world-wide would probably look something like this:
The former magical colonies, while completely accepting of muggleborns, are more likely to fall to the much stronger nationalist political tendencies that their recent colonial past would stir up - especially when you consider mages' greater longevity. This would put strain on the Statute of Secrecy, as the nationalists would be much more likely to come to the defense of their muggle counterparts if war were to break out. European pureblood society, which would have traditionally tried to strongly put a check on any attempts to break the Statute, would have lost those people most interested in doing so. By the end of the century, and likely before the middle, some war somewhere would provide enough motivation to the nationalists to break the Statute entirely, leading to the eventual political takeover of magical governments worldwide by the muggle ones (though time-lines and methods would vary), a renewed arms race with mages being given a lot of incentives to join their country's armies, and the worldwide situation degenerating into generalized civil strife while governments try to use mages as a panacea to their fiscal and societal problems.
From there, who can say where society would end up? I suppose it would be up to the author.
Of course, these are just my own thoughts on a completely fictional history, and I'm only a History grad student, what do I know?
