Standards Compliant websites using valid html and valid CSS need conditional
comments for their CSS layouts and fixes for the numerous IE bugs (hacks
ruining the layouts with IE 7: ie 7 does not apply the star hack but applies
the first child hack).
Browser sniffing is a serious problem when you mirror a site, much worse than
conditional comments.
I've never had problems with inline conditional comments or linked css between
those comments (apart from background images) and if a linked file is missing,
adding its address in the urls to mirror fixes the problem.