Be aware that this is a difficult topic.
You may encounter resistance even to the idea of running this panel. Resistance may come in the form of "we shouldn't talk about rape", "that doesn't happen here", all manner of things. This is not a silly funtimes thing. :)
Choose your moderator and panelists wisely.
We are familiar with the way this went down at Wiscon '09. That was very much a moderator issue. If you're going to run a panel about rape, it is vitally important to choose a moderator who
a) can moderate; by which I mean can guide the conversation in a constructive way and prevent derailment to the best of their abilities
b) has direct experience and training regarding how to talk about rape.
I recommend contacting your local rape crisis center. Many of them have a community outreach branch, and it's quite possible to find an SF geek right there! Our community outreach volunteer program alone has four people who regularly attend area cons, and several more who aren't that hardcore but would love to do something like this anyway. The people at your local rape crisis center are trained to manage these conversations. This is the best way to ensure that your panel is constructive and not destructive. Get someone with training. I could repeat this all day. It is very important.
Equally important: your choice of panelists. Even the best moderator is going to have a hard time of it if the panelists repeatedly derail. If your con's structure allows for your moderator to select their own panelists, do that. I've moderated this panel thrice, and chosen as fellow panelists other RCC volunteers, social workers, and writers who I know understand the importance of discussing the topic in a constructive way. Each time, we've gotten great feedback. Pick the right moderator, and trust them.
Derailing is damaging.
One of the things about this topic in particular: There will be survivors in the room. I mean, there are survivors in every room of every panel at your con. But in this room, there are survivors who read the panel description, made the informed decision to come to the panel, and in many cases had to gear themselves up to handle this conversation. This is why it's extra double bonus important to stay on topic. If your audience came to discuss rape in genre fiction and one of the panelists launches into an impassioned and victim-blamey defense of Roman Polanski, that is going to be triggery, and it's not what they signed up for. With this topic in particular, you have to discuss what's in the panel description and related, non-triggery things. This is, again, why you need a moderator with training, so they can navigate around things that are known to be triggery or to lead to triggery areas. It's easy for inexperienced people who just want to spout off about rape, and how X is not really rape, and how Y was asking for it, to pull the whole panel off-course and re-traumatize half your audience. Which I am pretty sure you do not want!
Set ground rules.
The rules I use for my panels on this topic:
a) This is not a place to discuss our personal experiences with sexual violence.
b) Rape is not a Thing Men Do To Women. Perpetrators and survivors can be of any gender. Please avoid using gendered language.
I send those rules to panelists beforehand, and I state them at the beginning of each panel. They're important. It's tempting to discuss our personal experiences, but that is a HUGE derailment and a series of landmines for the audience and your fellow panelists. And I know that many of us have grown up with the cultural narrative that rape is always Violence Against Women, but that is not the case. It's true that most survivors identify as female and most perpetrators identify as male. But there are survivors of other genders too, and their experience is erased far too often by that cultural narrative. (There are also perpetrators of other genders, of course.) Be respectful and inclusive.
Despite your best efforts, this is likely to stir something up in someone, and they're going to need to explore that. Please obtain brochures from your local rape crisis center and have them at the panel! Have your panelists make it clear that the rape crisis center's hotline is a great resource, whether they're triggered or just want to touch base. This helps keep your panelists from being cornered at parties all weekend and pressed into counseling service! Boundaries are important.
That's all that occurs to me right now - I'm undercaffeinated! I hope that concoms find this useful. Those who've attended or paneled at a "Take Back the Sci-Fi", please feel free to chime in!