Alexia and Eirene, was it a specific romance line that needed to be followed? idk that I should even call it a romance...this is quite disturbing to me and I'm not joking at all right now.
It's only with specific romances and if you specifically choose to play as an evil character. The rape is never shown, only demonstrated with dialogue options followed by a fade-to-black.
There are two Sith storylines; in each of them, the main character has the opportunity to corrupt a female Jedi apprentice and bring her over to the Sith.
The Sith Warrior's apprentice, Jaesa Willsaam, can be corrupted in one of two ways. She can be convinced 'logically' that her Jedi master is evil (true) and that the Warrior is a good person working to change the Empire from within, and that her powers and her compassion are best suited to help the Warrior. This Jaesa is called 'light-side Jaesa', and she's basically the same as she was with the Jedi: a good person who responds well to good people and who avoids romantic attachment. (Disturbingly, she may offer to be a male Warrior's baby-factory-without-a-romantic-relationship, because the Warrior's bloodline needs to be continued and more good Sith need to be created or some similar garbage.) Alternatively, the Warrior can basically mind-rape/brainwash Jaesa into being evil. 'Dark-side Jaesa' has sex with and/or kills everything, and takes unusual delight in torture: the model Sith apprentice. She is a romance option for a male Warrior.
The Sith Inquisitor's apprentice, Ashara Zavros, doesn't have quite the same amount of reactivity (partially because there is less difference between LS and DS Inquisitors compared to LS and DS Warriors), but the same basic outline of a relationship is followed: she's an apprentice who generally goes along with whatever the boss says, either good or evil, although 'non-pragmatic' evil generally gets demerits from her. The master-student relationship can be abused by a male Warrior to start a romance with her.
The Sith Warrior also gains a companion named Vette, an enslaved Twi'lek. The Warrior can choose to either treat her as a slave or as a friend: the key decision point here is her shock collar, which must be removed to get 'friendship' relationship. A dark-side male Warrior can abuse Vette by forcing her to watch him have sex. Any male Warrior can also start a "romance" path with both a friend Vette and an enslaved Vette. Any sexual relationship between master and slave is rape, and dialogue between them points this up.
A female Sith Warrior also has the ability to sexually abuse her underlings. One of her companions is a military officer, Captain Malavai Quinn, who is a potential romance option. Initial efforts by the Warrior to start a romance with Quinn may meet with refusal: Quinn, quite rightly, states that a relationship would be improper for both of them, that it would violate the chain of command, and that he's unwilling to deal with it, regardless of whatever feelings he may or may not have for her. The Warrior has the option to order him into bed despite his protestations. If this option is not taken, Quinn will, several conversations later, decide "screw impropriety" and confess to her anyway.
To reiterate: this is a specific subset of romances for a specific subset of characters, and not all of them
inherently involve abuse; in most, the abuse is a choice or choices the player can make or avoid. But the options are there, and they can be taken, and judging from the SWTOR message boards, many, many people have done so.
But enough of that: I'm done with squicky SWTOR for now. Back to Sera!