Consider the following:
EMH: There's no doubt that Seven was the victim of a sexual assault.
JANEWAY: How is she?
EMH: As well as can be expected. She's regenerating in her alcove. I predict her emotional recovery will take some time. I certainly hope you intend to hold Kovin responsible for what he's done.
JANEWAY: First I want to know how much of her story we can corroborate. Tom, you were with her on the planet. How long was she alone with Kovin?
PARIS: At least two hours.
JANEWAY: And when she came back, did she say anything about what happened?
PARIS: Only that they'd finished their work on the rifle. She seemed fine.
EMH: Clearly Mister Kovin used some artificial means to suppress her memory of the event. That would explain the unusual brain activity I found in her MRI scans.
JANEWAY: Did you find any other physical evidence of the... er... activities she described?
EMH: No. I suspect Mister Kovin used Seven's own nanoprobes to repair any cellular damage. She distinctly remembers Kovin activating them.
TUVOK: You seem to be accepting Seven's recovered memories as fact.
EMH: Are you suggesting otherwise?
TUVOK: Historically, recovered memories have often proven unreliable.
EMH: Yes, in cases where a traumatic experience has been repressed for years. But we're dealing with a very recent memory here, that was blocked by artificial means. When I removed that mechanism, Seven remembered everything that happened.
TUVOK: Human memory is rarely perfect.
PARIS: What are you saying, Tuvok? That Seven is making this up?
TUVOK: No, but we must remember that she's experienced hallucinatory images before.
EMH: That was in direct response to a signal from the ship where she was assimilated. She's not having hallucinations now. She's remembering what happened to her. I've confirmed this by analysing the specific brain activity in her memory cortex. We're not talking about conjecture, we're talking about science.
JANEWAY: Let's not get bogged down. Seven's made serious accusations and I won't dismiss them. If Kovin assaulted her, either as some sadistic attempt at revenge or what have you, we can't stand by and do nothing. Doctor, I want you to keep searching for any physical evidence to back up Seven's claim. I will talk to Kovin. Dismissed.
[Ready room]
KOVIN: This is offensive and absurd. She's obviously lying.
JANEWAY: Why would she do that?
KOVIN: Maybe you can answer that. She's your crewmember. First she attacks me, then she invents these ridiculous stories, and you try to place the blame on me. Is this some kind of negotiating tactic?
JANEWAY: I have no hidden agenda. I'm simply trying to clarify what happened.
KOVIN: I told you already. We went to my laboratory to adjust the guidance system on the particle beam rifle.
JANEWAY: And that took two hours?
KOVIN: She insisted absolute precision.
JANEWAY: We've confirmed that Seven was exposed to an intense thoron discharge.
KOVIN: She was, after the rifle's power cell overloaded. We reported the accident immediately.
JANEWAY: She now remembers that you fired the weapon at her deliberately.
KOVIN: That's preposterous.
JANEWAY: The Doctor now tells me the blast could have been enough to render her unconscious.
KOVIN: But it didn't. We were both startled for a moment. And after I apologised for the accident, she asked if I had a dermal regenerator, which I did, and I used on her arm. The one with the mechanical implants.
JANEWAY: Which you recognised as Borg.
KOVIN: I was aware she'd been a Borg. She told me herself.
JANEWAY: Did you ever express any animosity towards her? Any resentment of her Borg origins?
KOVIN: No.
JANEWAY: You never considered she might deserve some sort of punishment?
KOVIN: Punishment? Is that what you think I've done?
JANEWAY: There are many in the galaxy who believe the Borg are predators, users of others. You wouldn't be the first person we've met who felt that a Borg drone should be made to suffer the same way their victims have.
KOVIN: I never touched her, Captain!
JANEWAY: I'd like to examine your laboratory to be absolutely sure.
KOVIN: No. This has already gone too far.
JANEWAY: Then I'll have to contact the authorities. Maybe they'll be more helpful.
KOVIN: Are you willing to risk our trade agreement all on the basis of one crew member's delusions?
JANEWAY: Yes. Now, are you going to cooperate with our investigation?
KOVIN: I don't seem to have much choice.
The subtext in "Retrospect" is so un-subtle that you could easily drag it out to Full Frontal just by changing a few lines of dialog. But Voyager has to wink and nod its way through that subject, which makes the entire issue both uncomfortable AND poorly handled.
So what would that episode have been if Seven of Nine actually believed that Kovin raped her? Not a whole lot would actually change, but it opens the door for a somewhat darker revelation that would change how Seven of Nine -- and the audience -- thinks about what the Borg are actually doing to people when they assimilate them. Which, squickily enough, dovetails right into the Borg Queen's shenanigans in "First Contact", in trying to assimilate Data and Picard starting with their boners.
And here's where it gets REALLY twisted: if they'd really had the balls, they would have done this episode WITHOUT some alien-of-the-week scientist and made the accusation against, say, Chakotay or Neelix. Then Seven has to try to figure out how to move on from making such a horrific accusation based on a false memory and the guy she accused now has to figure out how the fuck they're supposed to ever work together again after something like this. The conclusion is the one we all know, and the one we all shy away from because WE are not the evolved humans that Star Trek is trying to show us: Seven sits down with the accused, meet face to face, and apologizes. The guy she accused nods, says "I read the report. I understand what happened. I don't blame you for what happened, I forgive you and all. But also, for the record, I think you did the right thing...
this was a false alarm, but the next time might not be. Just promise you won't let anyone ever put you in a position like that again. Not even me."