The seriousness of displaying the compatibility mode button should not be overlooked. An end user unknowingly clicks it and your whole domain is rendered as IE7 for them!
The cleanest way to address this is setting the X-UA-Compatible header in a server config. html5boilerplate now sets it in .htaccess https://github.com/h5bp/html5-boilerplate/blob/master/.htaccess but how can we address this within a deliverable theme?
A few workarounds, like a second html tag or an empty conditional comment are explained here http://nicolasgallagher.com/better-conditional-classnames-for-hack-free-css/ but concludes the cleanest method is a server-side config.
This isn’t just about Zen, but any theme that uses html5boilerplate’s method of IE conditional classes on the html tag.