Filia also mentions it when Rangas talks about taking her virginity. He makes her apologize for being a virgin, and she mentions how she hadn't had time to "do that, yet," which also implies that she knew beforehand. The Nan of the village also implies in the Prologue that she'll have to get used to doing something all the time soon. Then there was the scene in the bar in the Prologue where Filia was going to show some skin, but Marie interrupted them. She went into a kind of trance, and after Marie interrupted, she said, "What was I doing again?"
As for the Magic aspect, it's quite clear in the dialogue that Ragnas is using Healing Magic on Filia so her body can handle the punishment, not brainwash her. She's already predisposed to this behavior from the earlier clues. She also mentioned at the grave how she resented her parents, so I'm guessing they were grooming her. The years of normalcy with Marie and Mars after her parents died basically covered up her grooming until Ragnas showed up and started fucking her. It's also implied in her expression in the Super Happy Ending like you speculated, that once she started having sex with Mars in that world, she turned into a super slut again, because it was like a trigger to her upbringing.
The real takeaway to understand, though, is that none of the endings are real. Mars died. He was murdered by Black Knight Elina. The demon or dragon spirit or whatever "The Ancient One" was in the ruins basically sent his soul to an eternal "paradise" of Mars' making as a reward for breaking the seal. The real world, the village with the super sluts constantly participating in orgies all day every day, still exists and is the real ending. I wonder if Filia or Marie even care when they go home and find his dead body outside his house. They probably shed crocodile tears for 2 seconds before Rangas and Able stick their dicks into them again, probably right there next to Mars' dead body.
Super depressing...
