I do not know what features your Aux-in adapter gives you.

If the aux-in adapter does not put out a signal line specifically for this purpose, then you might be out of luck.

However, if the adapter *does* have a signal line that goes high when the "CD Changer" option is selected on the stock head unit, then yes, you're golden, just hook that up to the ignition-sense line on the empeg (instead of hooking the real ignition-sense line to the empeg) and you should be good to go. Make sure the yellow (constant power) line on the empeg is still connected to the car's constant power line of course.

Another option would be to use the empeg's phone mute line for this feature. There are some configuration tricks that will allow the empeg to pause when its phone mute line goes either high or low.