People being a bit creeped out by Margaery/Tommen was definitely a thing. Kid looked about 13.
You were meant to feel uncomfortable by Sansa being raped .. that's the whole point, it's a horrible brutal scene. Everyone understood it was uncomfortable and horrible, I don't think anyone was enjoying it.
The reason people felt uncomfortable by the Arya sex scene is because we've watched her grow up on screen, so we view her as a child. She still has a serious babyface going on and looks about 15/16 which means that people find it tough to see her in a different kind of light. I don't get why that's so confusing to people, it makes perfect sense.