Rapists are not rational.
"As long as the penalty for rape is less than the penalty for murder, there is no incentive for the rapist to kill. Once the penalties are the same, it is to the assailant's advantage to eliminate the victim/witness, since doing so can reduce the likelihood of later identification and conviction."
This is demonstrably untrue, in every sense. Potential penalties have little to no effect on criminal actions. It's disturbing how people constantly infer rational motives for irrational acts. Many rapists do kill their victims, despite the fact that the penalties for murder are much higher than for rape. Violent criminals don't stay up at night doing cost-benefit analyses and risk-reduction planning for their next attack. (Only organized criminals, aka polititians, do that sort of thinking.) They're driven by irrational impulse, and if they do even think about the possibility of being caught, they typically believe that they're clever enough not to be. There is no recorded instance where increased severity of penalties caused an increase in violence. They are invariably the result of increases in violence.
And in any case, killing the victim doesn't reduce the likelihood of being identified and arrested. In fact, chances are that it's just the opposite. Murders, particularly those with aggravating circumstances like rape, are treated as a higher priority by most law-enforcement organizations; and the vast majority of rapists and murderers tend to leave quite a lot of personally identifying evidence behind -- increasingly so as technology improves. On top of that, in the US, there is no statute of limitations on murder. There is, however, in the marjoity of US states, a statute of limitations on rape of an adult, (although typically none on rape of a chlid or minor). Limits vary from 1 year to 20 years, with the average being 7 years. Furthermore, in some states, murder committed during the commission of another felony (such as rape or armed robbery) is an almost automatic death penalty if convicted.