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From the view of the victim:

Rape is probably perceived as worst because the victim has to live with that experience/mental trauma that may occur. With a murder it happens and the victim is dead, the end.

Though to make a philosophical judgement you would have to look at all the people involved, and that would extend to friends, family, acquaintances, victim.

Theoretically we'll say the rape victim/murdered victim have lead similar lives, have made an imprint on the same number of people/same difference in the world. Does death or rape affect them more? I would guess death takes a greater toll, simply for the fact it has a long grief process for everyone.

Also when you break the question down further into the different types of rape, and consider Romeo and Juliet laws, among other things. It can become trickier to decide.

Rape vs. Death, death will always have a tremendous impact on everyone involved, I think rape, although a terrible thing, is more of an individualized recovery process and doesn't have as big as an impact.

Then we look at

Natural/accidental Death vs. Murder:

I think we would conceive the taking of a life is far worst then simply just a death.

I'd say that rape is worse. 9 out of 10 times a murder is committed it is publicly known, reported in the press and justice carried out. The families then have to live with the lose of their loved ones. However, when rape is committed a large amount of the time it is not known, reported and the perpetrator is still free. The Jimmy Saville enquiry and subsequent investigations showed how many abuses went on over years. Prostitutes have reported rapes but were ignored & even girls with fragments of memories due to date-rape drugs. Then of course there is the mental scars of the women that have been raped and the distress to their families.