The question of how intimately Windows and IE are tied together is a longstanding one, and in fact was a central issue in the antitrust case against MS (http://en.wikipedia.org/wiki/United_States_v._Microsoft_Corp...). The question was discussed at length in Judge Thomas Penfield Jackson's findings of fact (http://www.justice.gov/atr/cases/f3800/msjudgex.htm):

In contrast to other operating system vendors, Microsoft both refused to license its operating system without a browser and imposed restrictions — at first contractual and later technical — on OEMs' and end users' ability to remove its browser from its operating system. As its internal contemporaneous documents and licensing practices reveal, Microsoft decided to bind Internet Explorer to Windows in order to prevent Navigator from weakening the applications barrier to entry, rather than for any pro-competitive purpose...

Microsoft's executives believed that the incentives that its contractual restrictions placed on OEMs would not be sufficient in themselves to reverse the direction of Navigator's usage share. Consequently, in late 1995 or early 1996, Microsoft set out to bind Internet Explorer more tightly to Windows 95 as a technical matter. The intent was to make it more difficult for anyone, including systems administrators and users, to remove Internet Explorer from Windows 95 and to simultaneously complicate the experience of using Navigator with Windows 95. As Brad Chase wrote to his superiors near the end of 1995, "We will bind the shell to the Internet Explorer, so that running any other browser is a jolting experience." ...

Starting with Windows 95 OSR 2, Microsoft placed many of the routines that are used by Internet Explorer, including browsing-specific routines, into the same files that support the 32-bit Windows APIs. Microsoft's primary motivation for this action was to ensure that the deletion of any file containing browsing-specific routines would also delete vital operating system routines and thus cripple Windows 95.

So while it was originally a marketing decision -- the two were tied together specifically to put competitors at a disadvantage -- the implementation of that decision was not just marketing. It was implemented technically too, to the point where removing IE from a copy of Windows would break the OS. So regardless of the motivation behind the decision, the fact remains that the two things are tangled up with each other quite deeply.

Microsoft could have gone back at a later point and un-tangled them, but that would have been a huge project, and there was no real motivation for them to do so -- the settlement agreement that ended the antitrust case didn't require them to, and the market wasn't rejecting Windows with IE tied into it. So it stayed tangled up.

The big irony is that by tying the OS and browser together to get an advantage over their competitors, they ended up disadvantaging themselves. Those competitors can now turn out new versions of their browsers at a fast clip, because they're not tied to any release schedule other than their own. IE is tied to Windows' release schedule, however, so it improves at a glacial pace compared to other browsers, making it less competitive over time.