Solution?
How about adding this to the GPL:
Distributing software licensed by the GPL over a channel which, through technical means, blocks copying otherwise permitted and otherwise required to be permitted by this license, does not constitute a violation of the GPL, provided an indication is provided of how those blocked from copying the software through that particular channel may copy it in another fashion. The responsibility to provide such an indication does not fall on a distributor which did not initiate the distribution of the particular software in question.
Which means: Microsoft is not in violation of the GPL for limiting all software, even software bought for $0.00, from being copied between devices, if somebody puts GPL software in their app store. Neither are you if you put some GPL software there, as long as you include a notice that says, "Can't copy from your device? Go and download it again, you klutz".
Microsoft's lawyers are happy, the free software movement is happy, and everyone can just go back to sleep.