I hate to sound heartless here, but I don't think that the crew of the Pegusus have believed that they have done anything wrong. To them (and to the Galactica), cylons are not human. No human=no rape. Plus Lt. Thorne stated to Baltar that she had killed 7 men, if I remember correctly.
The thing I liked about the episode was when the Galactica deck crew was getting noticeably upset when the crew of the Peguses were making jokes about "taking" her. I think Galactica's crew has finally started realizing that these Cylons are more than machines. Balar was more than noticably shocked when he was taken to her on the Pegusus.
I think that is part of what this episode was about. If the "evil" Cylons are not machines but something more, then who's actions were the true evil? Just my 2 cents...