Stormblood isn't even the only occurrence of rape in the game either, instances of sexual abuse on npcs (usually by men towards women) has been a part of the game's story since ARR's launch - the very first dungeon after all (Sastasha) is full of women whom the Serpent Reavers abducted from villages and towns the pirates pillaged from and enslaved - one (optional) part of Sastasha is the disturbingly named 'The Hole' which is a cell full of women they've turned into sex slaves - one of these poor women even pityingly pines "I'm not one of them! I swear on what little virtue I have left!", hinting that she is being raped repeatedly (even more horrifyingly, these poor women never even manage to escape - they're mutated into lamia by the time of Sastasha HM and plead to be put out of their misery). It should also be noted a lot of the Serpent Reaver pirates are actually women themselves (including one of the guards of the aforementioned 'Hole').
Then there is Glaumunt's sad story during the lead up to freeing Minfilia and the rest of the Scions from Garlean captivity at Castrum Centri, where he reveals how the Garleans raped his mother and sister repeatedly while they were in a Garlean gulag in Ala Mhigo, so much so that they ended up killing themselves rather than suffer any further.
So it is not just Stormblood that rape is referred to as occurring. Either way, it should be clear that SE most definitely are not condoning rape against anyone, rape is an absolutely horrible thing regardless of who it's afflicted on, man or woman, but sweeping it under the rug and pretending it doesn't occur in a setting that is clearly dystopic only serves to make such acts look acceptable, which they most definitely are not.
Every time rape is mentioned in FFXIV it's always shown in a disapproving or negative light, to make the player sympathize with the victim and hate the perpetrator, it's never blaming the victim for it or to make the perpetrator look good. And the references to it in Stormblood are no exception. Rape is absolutely evil and horrible, but to pretend it doesn't happen in a fictional setting like Eorzea is simply ignoring the elephant in the living room.