I think when/if the next book comes out, Jon's rebirth will be different but yes, it's been obvious for a while.
They're obviously going to use the Bran visions to show flashbacks to the rebellion and The Tower of Joy. I guess Howland Reed might not appear in present day then.
It's interesting to note which storylines get completely cut from the TV series though as they're clearly not that important in the book.
It was also interesting to note the Greyjoys are back this series so book readers will know what that will set off. Indicates to me that the story there has some importance.