Been a while since I watched the first season but wasn't Danaerys' wedding night very rapey too?
Anyway, I don't think there's really a problem having a rape scene in a tv show. Problems only arise if a) there's confusion as to whether it was supposed to be a rape scene, b) there's confusion over whether the director actually understands what is rape and what isn't, and c) it feeds in to perceived enthusiasm for unnecessary violence against female characters.
Plus people saying "there is way worse on the show" are sort of missing the point. All the murder, torture, child cruelty and everything else is indeed worse but at least everyone accepts that it is what it is. Nobody argues that the Red Wedding wasn't really murder, or that it only started out as murder before turning into something else.
Unfortunately there is much more ambiguity around what people consider to be rape and what they don't though, so it's hardly surprising there's more of a reaction when the TV show (inadvertently) reflects that ambiguity.