Let's just get the obvious out of the way. Rape is bad. Depictions of rape are bad. However, this show put up a disclaimer just before the scence to be sure the kiddies are out of the room. If you are going to have to insert a rape storyline, then the least you can do is warn people. This show did that.
The arrival of the Pegasus has been expected by anyone who knew anything about the original series. Michelle Forbes (of Star Trek:TNG and 24) is "Admiral" Cain. Obviously the two crews were going to butt heads. Who knew they were going to play the Pegasus as a band of loonatics and power freaks?
This all escalates to a killing and an instant court martial. Apparently on the Pegausus, the accused are to sentenced, tried, and hanged.
This show is looking for a new arc right now. This may be the beginning of it. If so, let the good times roll.