I watched the season (and, in all likelihood, series) finale of Dollhouse earlier this week. My initial reading stands, I think, though it now appears to me as though the primary allegorical (and the premise and characters are more complex than mere allegory warrants, so this isn't intended as a comprehensive reading in any sense) import of "the Dollhouse" is as a representation of patriarchy, and the enforcement of rigid gender roles in particular.
That is, the feminist critique of capitalism is present (for example, in the commentary on the entertainment industry, and TV in particular), but it's more focused on the specific problems posed by patriarchal gender roles. The following musings contain many spoilers for the entire season.
The first indication of this is the name of the Dollhouse itself: the term "dollhouse" is certainly evocative, and does reflect the status of the Actives as mindless playthings, but it doesn't exactly make sense as a description of what the Dollhouse organization does in the fictional world. The organization bills itself as fulfilling clients' fantasies, whatever they may be. In contrast, an actual toy dollhouse is generally not seen as this kind of blank slate for a child's imagination to fill in freely; rather, it's a highly gendered toy, used almost exclusively by girls to act out (and rehearse) traditional gender roles.
Put another way, a dollhouse's immediate purpose is to allow a child to act out fantasies, but only of a very limited sort, while its larger purpose (not necessarily what it was intended for, but what it actually functions to do in the real world) is to enforce societal gender norms. Likewise, each Dollhouse branch is in the immediate business of allowing clients to act out certain of their fantasies, while there have been many allusions throughout the series to some greater project that the whole sprawling entity is working on.
The Actives under this framework are those whose true personalities have been supplanted by whatever pre-programmed identities are forced upon them. This is directly analogous to people who quash their own true desires in order to take on externally mandated (and often conflicting) gender roles defined by the patriarchy. Some remnants of their true selves (Alpha's sadism, Echo's suspiciousness, Victor's crush on Sierra) might leak through, but by and large they are completely displaced by the personalities they adopt to satisfy the needs of those around them.
This dynamic is nominally voluntary: as DeWitt constantly reminds everyone, the Actives work for the Dollhouse under legal contract. But the narrative reveals that for many of them, their choice to join the Dollhouse was not much of a choice at all. Thus is one of the standard apologies for problematic gender normative behavior—people are free to do what they want, and if that means wearing miniskirts then so be it—explicated within the framework of Dollhouse.
It is appropriate then that while the Dollhouse employs both male and female Actives, the majority of them are women. This reflects the disproportionate negative impact of enforced gender norms on women while acknowledging that men suffer under patriarchy as well. (Perhaps also of interest here is how Alpha and Echo react differently when they come to be inhabited by all of their programmed personalities simultaneously: Alpha experiences this as a liberating rebirth into godhood and destroys his original self, while Echo has no interest in these false personae, desiring only to pay her dues in the Dollhouse to win back her real identity.)
Characters aside from the Actives demonstrate other ways of interacting with the system of patriarchal gender norms. The two major "good guys," Boyd Langton and Paul Ballard, disagree with the Dollhouse's purpose and methods, but neither offers much promise of being able to do anything to stop it. Langton tries his best to keep an eye out for Echo, but his complicity in the Dollhouse project limits his impact. While Ballard initially appears devoted to taking down the Dollhouse, he comes to adopt the mentality of a "white knight," occupied more with rescuing Caroline in particular than in undermining the larger operation (tellingly, it takes Mellie, herself trapped within the clutches of the Dollhouse, to recognize this self-delusion for what it is). It is no accident that these two sympathetic male characters also comport themselves according to the norms of typical masculinity, guided by self-righteousness and doing their talking largely with their fists.
Topher, in contrast, does not conform to traditional masculine norms, but his misanthropic egotism and contempt for the Actives mean that he helps uphold patriarchy nonetheless. He's an example of someone who would actually benefit from a world without patriarchy, but goes along with it because feeling superior to its victims is easier than challenging the status quo. An example of someone escaping the stringent rules of patriarchy is given in the character of Whiskey, whose mutilation liberates her from gender expectations (note she becomes a doctor) because she cannot be easily sexually objectified under patriarchal standards of beauty (this option for freedom is, again, no option at all; disfigurement should not be a prerequisite for membership in humanity).
The remaining two characters, Dominic and DeWitt, don't really seem to function at the same allegorical level as the Actives and the rest of the supporting cast. Dominic is abstracted to the point of being an out and out symbol: he's the government that recognizes the power of patriarchy as a potential means to some future end, and keeps an eye on its activities as a result. DeWitt doesn't seem to be much more than a somewhat hackneyed archetype, the ball-breaking ice queen. That's clearly a role fraught with all kinds of more or less interesting gender dynamics, but it doesn't seem to be much informed by the Dollhouse-as-patriarchy framework.
So that's my reading of the show's motivating conceit. If the series does continue then I would expect its themes to evolve with it, the way Buffy's "battling the demons of adolescence" premise gave way to more complex themes. But it would also be nice to see how the story that's been told so far would work out, as I would also expect it to be consistent with this allegorical framework.