I share the common emotion that this is awful and shouldn't happen, but I have trouble justifying it intellectually.
Let's say, instead of DNA, it was an outstanding bench warrant. It seems pretty clear to me that the victim should have the help of the police in apprehending the rapist, but should also be arrested for the bench warrant. You might disagree, but there's no solving the problem of both needing the help of the police and being wanted for crimes. Waiting a day to serve the warrant, out of respect? Does that help?
This is different, yes, but how different? What changes to the database should be made here? Completely separate victim and suspect lists? It's burglary this time, what if it was homicide?
Not that you can separate victim and suspect when processing rape kit DNA! Eliminating common subsequences reduces the entropy and makes matches harder, we share a lot of SNPs in common.
My complete disgust that this happened remains, but this is one of the gnarliest ethical dilemmas I've seen.