While this episode was, on the face of it, about the four actives and their needs, this was also about those running the Dollhouse and their particular brand of self-delusion. It would be very easy to assume that the audience is supposed to agree with DeWitt that the Dolls are better off as they are, and that the voluntary nature of their participation is a sign that they recognize it. But the character reactions say otherwise.
If this episode had come before "Echoes", it might have been less obvious that those running the Dollhouse were lying to themselves and each other. DeWitt is well aware that actives aren't always "volunteers", and that the nature of the memory-alteration tech can make it seem as if it were so. DeWitt plays the part perfectly, however, because that's her job.
Topher is less sure of his justifications, as seen when Echo confronts him. Topher tries to talk about how everyone volunteers, and how it's for their own good, but Caroline topples every one of his arguments. If anything, Topher has been deserving this little moment of terror since the very beginning, because he's treated the Dolls like toys. He needs to hold on to the idea that the Dolls were all volunteers to absolve himself of the guilt of using them.
Dr. Saunders, however, demonstrates the truth about DeWitt and those running the Dollhouse. The needs of the actives are not the focus, they are a means to an end. They are the weapon used against the Dolls to keep them in line. DeWitt uses those needs to bring the troublesome actives back in line, because otherwise, she can't use them to satisfy the needs of the clients. And that, in turn, would affect the bottom line of whatever the Dollhouse and Rossum are working towards, as seen in the previous episode.
Sierra's discovery makes it very clear that it's not about the Dolls. Sure, Sierra needed to confront the man who took away her power, but DeWitt allows this specifically to ensure that Sierra's agency continues to be subverted. In the end, Sierra will still be used and abused by the man who paid to have her turned into a Doll. Just as Caroline will continue to do the work of the organization she was hell-bent on uncovering, because those impulses were subverted to ensure she would do so. Victor's love for Sierra is a problematic distraction, and destabilizing to Sierra, so of course it must be dealt with and removed from the equation.
Mellie's situation is a little different, but she was also less of a problem from the beginning. Perhaps she really was a volunteer; after all, in "Man on the Street", it was clear that some people would willingly become a Doll if given the chance. But even in that case, one gets the sense that her tragedy was used against her better judgment.
One could make the assumption, given how the episode ends, that Dr. Saunders suggested this "solution" to DeWitt's problem in order to give Caroline the chance to contact Ballard. It would make sense that Saunders would want to bring down the Dollhouse after her experience with Alpha, because it would be natural for her to blame those who failed to see the consequences of their actions and choices. From what we've seen so far, the technology behind the Dollhouse is not exactly perfect, yet DeWitt and the others continue to act as though the constant "glitches" are routine. Are they really so surprised, then, that things went so horrifically wrong?
All that said, this is yet another episode where the writers attempt to subvert the audience by pushing them to be sympathetic to the people using the Dolls, even as they explore the depth of how immoral they all are. Sooner or later, there must be a point to all of it. The writers have created in the audience an intense desire to see this institution brought down. Perpetuating it, even while showing it to be terribly immoral in the process, only plays into the hands of those claiming the series is ultimately advocating all of it.