I think that when this story is discussed it's usually assumed that "boner" just means a particularly stupid mistake, and that nobody could have known what it would eventually mean. But the use of "boner" or "bone" as a double entendre wasn't exactly unheard of before that. Think of Bringing Up Baby a movie from 1938, that gets a huge amount of mileage from obviously very deliberate double entendres around the word "bone." (Cary Grant is first seen holding a dinosaur bone and saying "I think this must belong in the tail." That's not accidentally funny; that's deliberate.) So while I may be totally wrong on this, I don't think it's far-fetched to imagine that "boner" already had a sort of secret meaning by 1951, even if it wasn't generally known. It's sort of like -- and again, you can see this in Bringing Up Baby -- the way the secret meaning of "gay" was hinted at in song lyrics and movies for decades before it went into general public use.
Another one I've always wondered about is from Gilbert and Sullivan's Trial By Jury:
DEFENDANT: Is this the Court of the Exchequer?
CHORUS: It is!
DEFENDANT (aside): Be firm, be firm, my pecker.
This is a huge problem for anyone producing Trial By Jury now, but at the time it was a reference to the old saying "keep your pecker up," with "pecker" meaning "heart." On the other hand, this was W.S. Gilbert, a writer who once had a female character say (in the play Engaged) "what have I in common with tarts?" (She is referring, or thinks she's referring, to the pastries.) So I've never been quite convinced that there wasn't some kind of early, dirty meaning of "pecker" that he might have been aware of.