First off, I'm sure that this will get marked as flame bait, because it's easier to rate than to reply.
The point isn't really whether IE is too integrated with the OS or not - so what if it is? Personally, I hate IE, *but* a lot of Apple's success is attributable to the tight integration of all its apps with the OS, while *nix distros generally suffer from having too little integration.
If MS didn't have such a lion's share of the market, this would not be any more of an issue that it is with Apple. The reason it's an issue is because we've forgotten sportsmanship.
If you're losing in a game, you don't (or shouldn't) cry UNFAIR! Instead, you find a way to win.
If people think that a crappy browser being too is too integrated into a mediocre OS is unfair, then WRITE AN OS THAT PEOPLE WANT - after all, it's not like the bar is set that high with Windows.
It's just too easy to blame failure (in this case, failure to gain a majority market share) on unfair play. Unfortunately, those who spend their time pointing out why they can't win will never do so.