The point is that it is not independent in there is a clear, direct path for coercion in arrangements such as that. Did Al Gore have a hand in hiring you at Apple? Probably not, no, but could they have? Could they have you fired or at least influence the board against renewing your contract if you did something they didn't like? I think the answer there is yes.
The idea that a publisher would threaten a major profit center (because doing something like this is a good way to kill a journal) over one paper that mostly just says what form the consumer wants to engage with their content in is absurd.
Hell, odds are they didn't even know about it until it went to print. If then. In Education alone T&F publishes 250+ journals. I almost guarantee you they have well less than one staff member per journal. The metrics they care about are "Are you publishing enough papers?", "Are you making money?" and "Are your publishing metrics going up?"
"Does a submitted paper suggest that our digital strategy might be less important than traditional print, and I want you to jeopardize the reputation of your journal for it" is fairly far-fetched, especially with no evidence besides "Publication was published by a publisher."
The structure for systemic corruption is there and the best argument you can make is for "one paper". Yes, I agree with you - but that's not what we're talking about at all.