Concerning the time back then when Nao and Haru had sex - I wouldn't say it was rape at all, it seemed very consential from Haru's side. It was him in the flashback who fondled Nao's breasts out of his own accord, without being forced, and Nao fully enjoyed it. There's nothing to indicate that Nao forced himself upon him.
After the act, Haru was simply totally overwhelmed by having had sex for the first time and didn't know how to react. Possibly Nao hadn't planned for them to have sex and had only wanted Haru to fondle her breasts, but they both enjoyed it that much then that they went ever further, until they eventually had sex. Having been carried away, they didn't quite know how to handle it.
About why Haru was lying on his stomach: that was simply so they didn't have to show his "mushroom with cream"
With the maid "assaulting" Haru with her body in the side arc at the end, that wasn't rape either, or they wouldn't have been lying that peacefully next to each other after it.
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Originally Posted by Dist
Soo .. there's actually story in this anime ? I dropped it after second episode because : Sora is annoying and Haruka is lame. Now all I see are new posts in the news section at Sankaku Complex how Haru goes around banging different girl each day.
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You're really missing out big time there! Yosuga no Sora has a much better usage of the omnibus format than Amagami. If you're bored by lame stuff like kissing the back of the knee, this is the show to watch!
Haru is a better protagonist than Jun'ichi in Amagami, and there was only little of Sora so far, she'll only really have any noteworth screentime in her arc at the end. If you should still dislike her by then, you could simply skip it.