I don't think the FCC is arguing that they don't want people's own distribution running along side a WiFi device, but rather, as WiFi chipsets become more "Software Defined" - rewriting the code in them is essentially the same as "modifying the radio".
The best analogy are the RTL HDTV over-the-air capture dongles for software defined radios. Guess what? They're generic radios which only do TV decoding via software - so people write NEW code and suddenly you can use them to do (and I dare say ANYTHING) that any sort of radio receiver could ever be made to do.
This is okay (and legal) with a receiver - they just don't want to to happen with transmitters. What would happen if anyone could do anything they want on the airwaves?
The counterargument is going to be "but they're not cracking down on MODIFYING the radio - just leaving the radio OPEN to being modified". This is expressly prohibited (and has been for a very long time) by the FCC - long before software-defined stuff. Lots of devices like Family-Band radios (and other licensed transmitters) are REQUIRED to be manufactured with things like "non-replaceable antennas" - which make user-modifications more difficult, because they are prohibited (unless done by a [ham] licensed operator).
The system was down for backups from 5am to 10am last Saturday.