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If you cast your mind back to episode four of the first season, they actually made the scene where Kyousuke falls on Kirino worse by having him actually grope her chest and not look like he was about to, as it was in the novel. In the same season, they cut an entire chapter about Manami and a fair bit of Kyousuke/Kuroneko bonding was cut since they decided to change the events of Volume 3 from a story about fraud to creating an anime. And as has been pointed out, certain scenes have been cut or changed this season.
I don't believe their motive for doing this is to hint at any particular ending. Rather, they probably feel that the removal of certain scenes will make the anime more coherent and allow them to maintain the atmosphere they want to establish in certain episodes. If they decide to just go with a slap as Kyousuke's method of waking Kirino up next episode, they may do so to avoid mood whiplash.
Regardless, the anime is following the novel's story despite a couple of scene changes here and there. The novels have yet to rule out any ending, so you'd expect the anime to follow suit.
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