I'm one step from calling it bad writing then. I feel like it's much more Selebus fault for not making it clear than any player's input. The idea of Wires or whoever it was putting Molly's hymen back after losing her virginity, and then putting her clothes back too (instead of just having Akira imagine it being off) is bizarre.
If that's indeed what happened, and it was "revealed" to be so later, the reveal was also off from Sekai being "lol you raped her dude! you can totally believe me cause I said so!"
There's intentionally making things unclear, which is fine. And then there's claiming it's the reader's fault for not understanding something that was both unclear and bizarre in what's been done that one time and never again.