My guess is that Intel doesn't want a generation of hackers (some of which will go on to create "The Next Big Thing") getting used to using competitors' chips... e.g. Arduino (Atmel), Raspberry Pi (Broadcom), and BeagleBone Black (TI).
"I am from Intel, and on the Edison team. There were reasons for the GPU being fused out - namely that the use cases around what is intended for Edison do not need video. That said, it may not be that way forever. I'd love to hear from the community on what they think of this feature being enabled - lots of voices make it easier for me to sway opinion."