Well I was there for years, and it seems Apple legal should know more about this as a concern than most, and they clearly didn't lie to us about it being a concern for _them_. (Still consistent with your point: it could be their own fear/uncertainty/doubt.)
Perhaps legal decided the fiasco wasn't worth a protracted court battle, and PR digressions, and foisted the option of re-implementing missing modernized functionality on homebrew/macports, on purpose?
Well, I would tend to trust the FSF’s legal opinions about the GPL over that of Apple’s lawyers. Addidionally, Apple didn’t seem to have a problem with GPLv2, and GPLv3 is no more copyleft than v2 was. Finally, the “might be forced to release proprietary code” story is, while FUD, extremely well-known FUD, repeated for decades industry-wide by GPL naysayers, and would be an appropriate choice for a believable story to tell the programmer employees.
If Apple merely wanted to save on work and dump it all on third-party ports, why not remove packages outright or, for a period of time, make them available as official add-ons? Why, in that case, keep ancient versions as part of the OS? Why remove something as widely used as Samba, which as I recall garnered some criticism at the time? It seems likely to me that Apple has some other reason than that to remove all GPL-licensed packages.
Perhaps legal decided the fiasco wasn't worth a protracted court battle, and PR digressions, and foisted the option of re-implementing missing modernized functionality on homebrew/macports, on purpose?