I think there's plenty more going on with Penguin than a major adjustment to the link equity calculations. That alone would not require the complexity or calculation overhead of an independent algo. In fact, there is a lot of evidence that link equity adjustment is going on in an effort that is independent of Penguin.
Also, recent comments from Matt Cutts indicate that the Penguin algorithm has been undergoing major work these past months. Again, such an effort would not be needed if the Penguin algorithm were only about links. Yes, the link profile may be (and probably is) involved. But I'm predicting that when Penguin 2.0 finally hits, we'll see something very confusing and more evidence of Penguin's complexity.
I also see that some sites have recovered lost rankings and traffic by fixing their backlink profile, even though Penguin has not been revised or refreshed.