"Acton" Like a Fool (sorry)

I would have to disagree that Heywood outright refutes Whately's views on marriage. He calls them into question, certainly, but ultimately I think he finds common ground with Whately.
Take Acton and Susan's eventual nuptials, for instance. The moment Acton sees Susan he immediately disregards his "male" role as authority figure, instead falling head over heels in love: "I am enchanted," he says, " all my spirits are fled, and with one glace my envious spleen struck dead. (7. 93-94)" Acton, despite all of his fiery fury just moments prior, now seems to embody more Whately's "wifely" role, "favoring all lowlinesse and quietnesse of affection."
Susan, likewise, at first adopts the "husband" role, rejecting Acton's affections with a stern "Acton! Oh God, that name I am born to curse...See, I spurn his gold. (9. 52-54)" At this point, of course, Susan does not suspect marriage as Acton's attention, but rather a more base deflowering. At this point as well, Whately would be shocked to even consider a marriage between such figures, a "deformed family" would surely result. That Sir Francis is so adamant about his love and intentions for Susan certainly calls into question Whately's views; Heywood is saying that, gender roles be damned, Francis will marry her. And yet, the second marriage is actually proposed, Susan's attitude changes: "I will yield to fate, and learn to love where I till now did hate. (15. 147-8)"
By the end of the play, Frankford and Anne, who initially seem to embody Whately's proscriptions, have fallen apart, while the horribly mismatched Sir Francis and Susan are (admittedly tenuously) engaged and determined to make their marriage work. Nonetheless, in order to marry, Francis and Anne are forced to adopt at least somewhat Whately's roles. Though Heywood does not believe that Whately's rules necessarily make for a good marriage, he believes that some semblance of them must exist for one to work.