It might be true that users would have an immediately negative reaction to change; I suppose it's impossible to know for sure. But that doesn't mean that the new design wouldn't have been better at providing the functionality that Facebook purports to offer.
Even if you're right, there's a similar long-term-vision vs. short-term-incentives situation. The overhead of having to "learn" a new system (which is already and would have remained fairly passive and simple to use) becomes less reasonable to hate when amortized over years of improved performance.
I don't really use Facebook much and am agnostic about the extent to which one site or another would better serve users. It's ambiguous to me what Facebook truly sees as its function / purpose anyway, so the criteria is murky here.
But the argument in this article isn't necessarily assuming anything about what users want, rather it purports to know from a design perspective what will ultimately serve them better.