I think Joss, Tim etc. address difficult subjects in a way which is fundamentally liberal, but cut with irony and at least a nod towards moral complexity. I've posted before about how I think they can overshoot sometimes - in a nutshell I think Joss Whedon's ironic playfulness around liberal values can be taken as unironic support for right-wing values of various kinds. It is taken as such by Libertarians and racists, because I've read 'em on the web.
I think this time, from this description of the episode, they would have misjudged.
The episode opens with Mal and Inara fighting (as they do). Mal tells Inara she pretends to be a lady and wants everyone to bow before her and kiss her hand but she’s just a whore. Then the Reavers attack and take Inara. While trying to get her back they learn that she had something that would make anyone who had sex with her die. (BTW I think this 'something' was what she was preparing to inject in that episode)
When they finally track down and board the ship they find all of the Reavers dead and Inara shaking and traumatized. They take her back to the ship and Zoe guards her room. Mal tries to get in to see her and Zoe tells him he’s the last person Inara needs to see. He pushes past her, kneels before Inara and kisses her hand.
I know what they are trying to do here, and they are trying to do something that could be positive, but I think this misses by miles. I think it's hard for a person to step outside their own culture, and sometimes you might think you have done it, but you haven't. An example to do with race would be to fall into the trap of making every black character super-good. It's still racist and patronising. It still fails to see black people as fully human. Firefly doesn't make that mistake, but I think this episode - if made - would have made a similar mistake.
One has to say for example, that being raped by a whole ship load of cannibals couldn't be an event in a plot arc, from which we move on. I know women do survive extreme sexual violence (as in Bosnia) and live, but it's not, I don't know what to say, it's not even like Mal being tortured by whatsisname and his heart stopping (which god knows he recovered from implausibly quickly).
And why does it have to be Inara? (I know in plot terms it's because she has the injection ready - but I mean in terms of series dynamics). Because she's 'a whore'? Because it makes Mal reconsider his ideas? I think this is another example of irony failing to work. Why out of all the crew would 'the whore' be raped? The reavers will, and do, rape everyone. Why couldn't it be Mal? What would that do to his attitudes? Why can't a man be redeemed through his own sexual suffering instead of the vicarious suffering of a sexualised woman?
What would an episode be like where any other member of the crew was put in the 'Inara' role? It would be different in each case. Think how impossibly awful it would be if it was Kaylee or Wash who was raped. Why is that impossibly awful to contemplate, and Inara not?
I suppose my overall feeling is that rape can be a subject for fiction, of course, but it has to be treated more carefully than this.
Further discussion at Alas a blog.