You can specify X-UA-Compatible as a real HTTP header (instead of using HTML's http-equiv in a meta tag), which will ensure it applies before any HTML/JS is output.
The simplest way is probably to set it at the front-end web server level - how to do this depends on your web server (e.g. Apache, IIS, nginx, etc), or you can use cfheader to do it with CF:
<cfheader name="X-UA-Compatible" value="IE=9; IE=8; IE=7; IE=EDGE" />