If someone purposefully hides salient facts from you in order to coerce sexual intercourse then it can be that consent was only acquired by deception and that under the law consent was not freely given. That seems a reasonable definition of rape.
A person seeking police advice may not know they were raped in that way. And prosecution despite that person's reluctance would seem right as it seems to protect the public from a menace (someone knowingly spreading HIV).
Those mightn't be the facts here, but save the last paragraph it fits with what you're saying and explains why a public prosecutor would seek a prosecution despite the alleged victim not considering themselves to have been raped.
If someone is familiar with the case and Swedish rape laws then I'd be interested in their input here?