In the introduction to "An Introduction", Foucault regards Freud's contributions to our understanding of sexuality with sharp sarcasm. He writes, "Have we not liberated ourselves from those two long centuries in which the histroy of sexuality must be seen first of all as the chronicle of an increasing repression? Only to a slight extent, we are told. Perhaps some progress was made by Freud; but with such circumspection...yet another round of whispering on a bed" (5). It seems that Freud's explorations of human sexuality only led to a confined, controlled distillation of human thought on the the subject. Rather, I think this is a 'general view' of ours that Foucault mocks.
Foucault confronts Freud's contributions to society more directly in the "Scientia Sexualis" section. In the opening, Foucault says, "Until Freud at least, the discourse on sex - the discourse of scholars and theoreticians - never ceased to hide the thing it was talking about" (53). Now the scientific will to know about sex is merely another control mechanism. Foucault identifies resulting trends: "the postulate of a general and diffuse causality" i.e. "the principle of sex as a "cause of any and everything" and "the principle of a latency intrinsic to sexuality" among others (65-66). All these ideas attack the fundamental propositions of psychoanalysis as tools for the further repression of sexuality instead of its freedom.
I believe the claim that Freud's obsession with the Oedipal syndrome, etc. gives sexuality undue power is pretty unsurprising. However, it drew me back into the ontological vs. epistemiological paradigm. Does the viewpoint of Freud's psychoanalysis represent a shift in human understanding that inevitably leads to our present attitude towards sexuality? Does the "postulate of a general and diffuse causality" parallel the breakdown of meta-narratives?
When you say "the viewpoint of Freud's psychoanalysis", are you referring to Foucault's critique of Freudian psychoanalysis, or to the tenets and practices of Freudian psychoanalysis themselves? In terms of Freud's work, I as well read this as being directly connected to what Foucault describes as the current rhetoric of a popularly repressed sexuality, as a sort of beginning of a discussion of sexuality that isn't "subordinated...to the imperatives of a morality" (53). Still a discourse of confession and normalization, but one that is more eugenic than moralistic, and doesn't seek to fall back on the old guidelines of morality to determine what is normal and what is aberrant. Also supporting your assertion would be the way that this discussion of sex is only appropriate in the space of the psychiatrist's office, so it's still compartmentalized in a way that would support a popular sense of repression.
In terms of the question of ontology vs. epistemology in Foucalt's writing, I feel it's a little tricky to tease the two apart. I read Foucault's thesis as presupposing that the ways that society thinks about sex do have an effect on our sense of identity, but also that there is something aloof and unaffected by these things about sex that gets re-explained and re-dominated over time, but never really fundamentally changed. So I wouldn't feel comfortable placing Foucault's portrait of society squarely on either side of that divide, but that's just me.
I read Foucault's description of "diffuse causality" as a sort of metanarrative implicit in Freudian psychoanalysis, since it seems to provide the motivating idea for many of its practices. Thus from my own reading I would say that it does not in fact represent a break from a unifying metanarrative, since Foucault goes on to claim that this overriding idea justified the thoroughness of the psychiatric confessional process, and must have tied together a lot of subordinate ideas about specific methods of analysis and symptoms.