First, there's no point in evaluating competing rumors about what Mingus did or didn't like; what's the point unless one or the other comments can be verified.
However, "not playing the changes" could mean at least two kinds of things.
It could mean not improvising at all, and I have heard one version by a classical musician that's basically a melody recital rather than a jazz piece.
It could also mean improvising using notes that don't seem to follow the chord progression - or not using the chord progression at all, and that latter possibility is what I'm hearing when I listen to Beck's version. Basically, he plays the head as a melody, and then he goes into a blues-rock jam that doesn't seem to bear any resemblance to the chord changes of the actual tune. Later he does come back to the tune, mostly stating the melody but with some dramatic rock guitar flourishes, still not really improvising over the changes of the actual song.
By the way, such practices have been common in jazz from the beginning, with the band often reverting to a 12-bar blues structure for solos (though not in this particular case) on a song that has a more complex structure for the head.
Now given that Beck plays something that is a fine rock-blues instrumental inside the tune, Mingus might well have enjoyed hearing it, but have also remarked that, indeed, Beck wasn't at any point improvising over the changes of Goodbye, Pork Pie Hat.
