I'm not saying it's a plot hole, per se, but, "any number of things could have happened" is not exactly strong plotting either.
For me, it never felt like a decision this character would make even when the wounds were fresh. It always feels like a decision Morrison made more for the story than for the character - which gets back to my larger point and skepticism about storytelling in general and especially corporate superhero comics.
Here, immediately after the battle, Hippolyta isn't seen wanting more revenge, but a way out of the violence of this world*.
She prays for a "paradise" for her and the Amazons, but, then what? Stops to cut off Hercules' balls just in case she wants them later? Even as an idea to use him as revenge against a patriarchal world, it is done so in a very patriarchal way; it may be daughters instead of sons, but it would still perpetuate his legacy, ensuring that he lives on. So, it's not exactly subversive storytelling.
*edit - "Sweet Aphrodite. No more spilled blood. No more shackles. Let us retire forever from man's world. Let us draw an impenetrable veil around our affairs and prosper in peace. In a world that bears no mark of men." This is does not sound like a woman that a) wants revenge, nor b) wants to have her attacker's child. Thus, that's why the story doesn't fit together very well as a whole.
And as to whether or not she was actually raped? It's pretty heavily implied that was the intent. It shouldn't take answering questions later on twitter to clear that up.