If you're going to do that for any browser, phrase it apologetically (sorry that my website sucks on IE6) or encouragingly (upgrade to get better features!), never aggressively ("upgrade from IE because IE sucks!")
And Never, Ever, use an alert message. If you're using an alert message, it's because your website is rubbish. Good websites give feedback inline.
IE6 might be a pile of crud, but your customers probably already know that. Nobody uses it out of choice.
Your website is there to help users. If you're going to punish them for visiting, they won't come back.
I would agree with your "not by choice" statement, but I've seen many computers that still have IE6 because the users are still on XP SP1 and never run Windows Update (or have so much malware that IE no longer runs, so they've switched to Firefox 2).
The site I've developed for work says
<url> is tested in the following browsers:
Microsoft Internet Explorer 8+
Mozilla Firefox 4+
Google Chrome 9+
Apple Safari 5+
While other browsers may work, you may experience display or functional issues. It is highly recommended that you upgrade your browser to the latest available version.
I don't exclude anyone, but the site does start looking pretty funky in IE6 and Opera.