Thinking about child rape specifically (since the Supreme Court just outlawed the use of the death penalty in such cases), I think my intuition is the same: troubles with the death penalty as applied notwithstanding, I don't have any intrinsic reason why child rape is not worthy of capital punishment. But on that score, Matt Yglesias makes a good point:
You want to make it the case that no matter what terrible things a criminal has done, he would get an even worse penalty if he killed the victim/witness. Getting bogged down into a debate over the relative heinousness of various crimes is a bit of a red herring -- there's an internal logic to the deterrent system that requires murder to carry a unique and maximally severe penalty.
A good (if not necessarily constitutionally-manifest) point.