Can the victim sue her attacker in civil court? Absolutely. Many states have a law that allows a conviction of such a crime to raise a presumption of guilt in a civil trial.
As far as the motel is concerned, suing them would be an uphill battle. Was the perpetrator an employee or owner of the motel? Did the motel know that the victim would be raped? Were the employers or employees complicit in any way? Without some indication that the motel allowed the rape to occur when it could have stopped it, I don't see how recovery against them would be possible.
Keep in mind that many personal injury attorneys will offer a free consultation. However, even if the victim can't find a good attorney to offer a free consultation, then she should pay for one with a good attorney if for no other reason than to answer her questions about whether or not she has a case that is worth pursuing.