In Dollhouse, there are three main types of identity: the original personality, the soul (base personality), and artificial imprinted personalities. Generally, the original personality and the soul are indistinguishable and are only disconnected when a person becomes an Active and the original personality is put in a wedge (hard drive). The wiped Active is then given the submissive and child-like tabula rasa default state and subsequent personalities are imprinted, but some aspects of the soul always show through. The soul is similar to the original personality but without its memories and can be considered a different person. Actives with multiple imprints (Alpha and later Echo) are basically souls in control of different persons with their own distinct personalities that they can slip in and out of. Alpha eventually manages to find an existence where his evil soul no longer calls the shots and the collective good of many imprints controls Alpha's mind.
The main concern about rape in Dollhouse is through the most obvious function of becoming an Active in which the original personality makes a deal to be wiped and then be made an Active to be imprinted for a variety of unknown engagements for a five-year term. The person can't possibly give meaningful consent to each of the sexual encounters that will be required during that time, so it's effectively rape of the original person by having their body used for sex. Of course, identity is a bit more complicated than that.
The second concern relates to the rape of the soul as a distinct personality. In the episode "Omega", soul-driven Actives Alpha and Echo take Echo's original personality Caroline (imprinted in a different body) to task for abandoning Echo. Alpha describes it as Caroline going into the wedge and leaving her body Echo to be ravaged by the Dollhouse. As Alpha and Echo see it, the original personality takes a vacation while a completely different person (sharing similar personality traits due to the underlying soul in the body when the original personality is in control) is then sold into slavery, making the original personality a rapist working with the Dollhouse rather than simply a victim of them.
The third concern is of the rape of imprints created to consent, which is a tricky issue because there is consent going on. The imprint does consent to sexual activity with the client, however, Topher programs them so they will consent, bringing the value of the consent into question. I tend to think that imprints are people, so even if they're designed to do something, they still make a concious choice to do it that should be respected. However, this consent does not always extend to the soul when the soul is capable of glitching self-awareness past the imprint boundaries. What I believe is the greater issue is that the imprint cannot truly consent when there disception going on where the client is pretending to just run into the Active etc., and the client would be raping them in this way.
A big question pertinent to analysis of Dollhouse rape is: Who owns the body? If it's the original personality, any sexual activity consented to by the soul or imprints would be meaningless. This is the argument usually put forth, but the series challenges this conceptualization.
Topher: "Don't you want to know who you really are?"
Claire: (pauses) "I know who I am."
--Episode 1x12 "Omega"Claire Saunders, an imprint, does not want to be replaced by her original personality. After Alpha killed the original Dr. Saunders, Topher imprinted an injured Active, Whiskey, with a personality tailored to be the replacement doctor. She functions for months before finding out she's an Active and then she's scared that she'll be wiped. She neglects to have her facial scars healed so that Adelle won't start thinking Claire would earn Rossom more money as an active Active, and with Boyd's urging tries to run away from the Dollhouse. Here, the imprint asserts an identity that is more deserving of respect than Whiskey's original personality because that person isn't in there anymore. Claire is, and she doesn't want to face what amounts to death for her identity, so she runs.
If Claire were to have consensual sex with someone (Boyd, say), I think it would just be consensual. The original personality couldn't consent, but she doesn't own the body anymore. Does she even have a right to the body? The Dollhouse would say she does... but the Dollhouse is slavery. To them, Claire is essentially a slave without rights. Outside Dollhouse morality--in my own morality--I would say that Claire has an inalienable right to that body given that the original personality wasn't there when Claire was imprinted. Unless Whiskey--the soul--longs for the original personality (unlikely, as she shows no signs of being advanced like Alpha and Echo), I don't think it's necessary to give her back her body. It's like Judith Jarvis Thomson's "violinist" defense of abortion, where it's a woman's right to kill someone to protect her bodily integrity than have them impose physical costs as her body is used to support their life.
What if they were both in there together? What about composites? Alpha and Echo flip through all their imprints while maintaining a general collective identity steered by the soul. Before the thought-pocalypse, Alpha has extreme difficulty keeping a handle on his imprints, and they all argue a lot. Echo's imprints tend to work together pretty well, but there is that psychopathic misogynist Terry that accidentially got inside her brain in "Belle Chose". Her soul puts in effort to keep the Terry imprint suppressed, but it's still there, and she can still phase in and out of it. If she were to have sex with Ballard, the man the soul loves, I'm sure Terry would hate it. He would not consent. It would effectively be raping him because he is forced to stay in Echo's body as a passive observer.
In the case of Terry, I don't think it matters because Terry is just plain evil and there's nothing redeeming about him. Alpha is the inverse, though, because both his original personality and his soul are evil, and it's the composited imprints that make Alpha good post-thought-pocalypse. You can't just point at the soul and say "that's the part that counts". The real answer is more fluid, based on context. It really is about who you think should be dominant based on your own moral values. I think Echo should be dominant over Terry. I think Alpha's good imprints should be dominant over his psycho sides. If the psycho killers are raped because of that, I don't really care. They are inherently beneath my respect on virtue of being psychos. It becomes trickier if we move away from the extreme represented by the psychopaths.
What if Echo were to have a good imprint that would never consent to having sex with, say, Ballard, but Echo the soul would? The imprint could be a lesbian, a straight man, asexual, or suffering from trauma that would make having sex with him really upseting. Would Echo be obligated not to have sex she desires because an imprint that would otherwise receive full respect has these kinds of issues? What about the other way, with the imprint acting against the soul's wishes? I don't have a good answer for that. Anyone have any thoughts?
Anyway, to wrap up, the issue of rape in Dollhouse is a lot more complex than most people realize. Though the show's narrative initially compells us to be sympathetic to the original personalities alone, it eventually explores more complex issues of idenity that really puts the notion of who has agency into question. I suspect the feminists who criticize Dollhouse rape really loudly never watched the show long enough to see that, and I think it's a pity.