The rape scene was definitely not like in the books, but the situation in the TV show was also different. In the books, Jamie had just returned to King's Landing after being away for so long, so he wasn't there for Joffrey's death. They saw each other for the first time while in the sept, and lustily went after each other. In the TV show, Jamie had already been back in King's Landing for perhaps weeks, was present for Joffrey's death (and was supposed to be protecting him), and he and Cersei had already been quarreling. So the sex scene in the sept took place under very different circumstances, and as such at least it makes some sense that Cersei did not consent (at first). Not that I agree with creating that scene, but that at least might explain it.
As for Margaery's grandmother, it was the same as in the books -- although in the books, grams doesn't come straight out and admit it like in the TV show. In the books, it was still Littlefinger who orchestrated it all, along with the grams, by using Sansa and Ser Dontos to get the poison where it needed to be during the wedding.
Coldhands. Yeah, that's basically the only person Bran et al met once they got outside the Wall, until they find the Three-Eyed Crow. But like someone else posted, I guess this is a way to introduce some drama into that storyline and to drag it out longer so they don't catch up as fast.
Man, that would suck if the TV show catches up and surpasses the books...