I find this hopelessly naive. Yes she said that. Why is she only pulling 1989? Not her other albums? It seems the most likely true answer is "because that one is still selling strong so it is in her interests to do so."
It's also very possible that Swift doesn't have control over where the other albums appear, since they're from old deals she made before she had much leverage.
Most likely, it's a combination of all three possible explanations: some albums are from old deals she has no control over, others (1989) she wants to make more money on, and she's also disgusted with Apple's treatment of artists and taking a stand.
People don't need a single pure motivation for their actions to be legitimate.