You can do that with Bartender, and I'm sure other action bar mods can do it as well. Simply click the box that says "click-through". Another option is using a cast bar mod or WeakAuras for instance to set up a gcd bar.
Originally Posted by rumbo
Re original poster tho: Simply make a new icon, go into Trigger and click Status. Then scroll down to Global Cooldown. Set a reference spell that's on the GCD (and if you want untick the Automatic Icon on the first page if you don't want it changing every time you click anything that's on the GCD).
Example, with a cute kitten icon: