SFGate[1] reported at the time that exactly what I said happened happened. IIRC Apple later mooted any regulatory action by reverting their developer policy change. But for a while, it was looking pretty sketchy. And I think it's telling that the Thoughts on Flash letter is no longer available, taken offline at around the same time antitrust suits started up again.
The decision to prevent Flash from operating on iOS was never considered as cause for lawsuit by any of the agencies mentioned by GP.