It's obviously "deliberate" but simply too hard to parse. Personally if I really insisted on the pun I would have put an extraneous comma that disambiguates:
>Controversial New Milk, Shakes Up Big Dairy
That still has the pun in it but at least would be readable. If people wonder why there's an unnecessary comma there they might realize the pun.
[1] https://en.wikipedia.org/wiki/Garden_path_sentence - which includes "When read, the sentence seems ungrammatical, makes almost no sense, and often requires rereading so that its meaning may be fully understood after careful parsing." Certainly true for me.
To 'shake up' is perfectly idiomatic. Using 'up' as a standalone verb is less common and should be your cue.
Like "the old man the boat," the combination makes it hard to parse. The cue is that you get to "the boat" and realize you misinterpreted it. The point was not that it was impossible to understand.