Well, to be fair, the controller (which is awesome, BTW), in no way jeopardizes or, potentially, jeopardizes other Xbox 360s. It is not a threat to the software/hardware security model of XBox Live or the 360. The intentional hacking of the PS3 and revealing possible system and network exploits, enabled through the OtherOS feature, is not the same thing as modding a controller.
To be clear, I really have no issue with Sony doing this if it is going to make their service to us more secure. I understand why some may be upset, but it's really not that big of a deal, for THIS particular thing.