John Dunbar
correct about everything
I could be wrong, but I just rewatched season 1 and I don't think he ever explicitly says that she was raped. He makes it clear that he abducted her, as does Bran later in the season. My expectation for GRRM putting a twist on the Tower of Joy is that Lyanna was happy with Rhaegar and loved him. Possibly that they were married (some Targs, maybe just Aegon, took multiple wives, right?), making Jon the rightful king when Dayne and the Kingsguard defend him.
They really should have been more explicit for casual viewers. Simply not splitting Ned and company fighting the Kingsguard and the Jon reveal by like 8 episodes would have probably done it.
i don't think that would be a twist at all. in fact, lyanna going with rhaegar willingly is pretty much how everyone expects it to have played out. so rhaegar not raping lyanna would be a twist for the people of westeros, but not for the readers. a twist would be something like rhaeger actually raping lyanna, and the "promise" ned made would be something like killing the bastard that resulted from it.