I has been, what, 15 years from those court proceedings. Don't you think it is possible the MSIE has been tied to the operating system in subsequent releases: Windows XP, Windows Vista, Windows 7 and Windows 8?
Sure it's possible, but then it wouldn't be so amazing that they had un-done it. Microsoft was, in those court proceedings, claiming that being integrated with the OS was a very fundamental part of IE that was not trivially undone.
AFAIK nothing much has changed since these days, but MS did add a option to remove the Internet Explorer directory in Program Files in Vista and note that HTML Help for example already depended on IE components even back in 1997.
