If the letter's going to be at all important later on, I'm sure they'll work it in. I don't tend to think it will be-- whatever Jon does after A Dance with Dragons
, it probably isn't going to be taking up the banner of the King in the North, and if all that happens is him refusing the possibility, that's not important enough from the TV writers' perspective to be worth dramatizing.
I imagine the order of King's Landing vs. Riverlands events in the book is likely to be jumbled a bit. If the show stuck very faithfully to the sequence of events in the book, they'd have to do Joffrey's wedding in the first or second episode of season four, and then the rest of A Storm of Swords
would only take up half the season. That might be the plan, but I doubt it. We already know, for example, that Oberyn Martell isn't being introduced this season, even though in the book he arrives in King's Landing before the Red Wedding.