My music theory professor in college told me: "Good artists copy; great artists steal."

From what I know about Fifty Shades, there are a million problems with it, but "it's obviously fanfic" is not one of them.  You wouldn't guess that Ana and Christian used to be Bella and Edward.  At most, you'd say they belong to similar archetypes.  If E. L. James took Twilight's characters and relationships, and then recast them into something that wasn't obviously a reskinned version of Twilight, then more power to her.  And more power to you if you want to do the same.  This is called "taking inspiration."   

The usual argument against derivative works -- when they don't take money out of the artist's pocket -- is that they piggyback on someone else's hard work.  But if you're worried about that, look at your own words:

Frau Eva wrote:

Probably put in a bit more character development, rework most of the lines, Americanize it, un-Ohtori-ize it in general, and of course the idea of what's happening completely changes when you take away the context of it being a continuation of something . . .

Maybe this story started as piggybacking on Be-Papas' work, but by the time you've done all that, you'll have earned your own pig.  Your characters and setting will be yours, as surely as if your story had started as an original work of fiction; in fact, starting from scratch might be easier than adapting what you've written.  Once you've done that, once you've made the story your own, I don't see how anyone can say that publishing it is immoral, any more than, say, Neil Gaiman is immoral when he writes and publishes Sherlock Holmes or Chronicles of Narnia fanfiction.