To answer the question in your thread title, there is no way to use the GPS receiver without having the phone radio on as well. Of course, those pop-ups are a nuisance, but a bigger issue is the use of battery as your phone searches for a signal. That's probably the biggest power hog of anything your phone does.
I have MotionX GPS, too, and would love to be able to turn off the phone while leaving GPS on.
If you've got $150 burning a hole in your pocket, you could get the Bad Elf Pro GPS unit, and have GPS on your phone via Bluetooth while in airplane mode.