You need to read the Bishops document from back when this happened.
catholicculture.org/culture/library/view.cfm?id=7836&CFID=11097112&CFTOKEN=16244596
The rationale, which I am not convinced about, goes that in rape, the sperm can be considered the product of an unwelcome agressor. The sin in contraception is not that sperm are killed or that ovulation is prevented. The sin is that contraception interferes with the unitive and procreative aspects of the marital act. In rape, there is no marital act - only a violent attack which happens to be genital.
Ending the life of a newly conceived child is always wrong, even in the case of rape. That is why the Bishops wanted to only give Plan B if a test confirmed that ovulation had not already occurred.