The funny and sad thing here is that Microsoft does not want the
standard compliant mode to be the default, and rather make it
and opt-in. Granted the reason is backward compatibility and such,
but still, the default is not standards, regardless.
What we do in core now (at least in garland) is to detect if IE6 or
earlier, and put out some specific CSS for it. No metas or other
stuff.
So, I say keep core out of this. No changes necessary.
There are several browser detection libraries out there, e.g.
http://techpatterns.com/downloads/php_browser_detection.php
You can download it, include it in template.php, and spit out the
appropriate meta if you so wish in page.tpl.php and friends.