***Spoilers*** Manami was right but she is still a terrible person

After watching the entire second season, it's clear who exactly is to blame for Kyosuke and Kirino becoming estranged: Manami.

In context, during the early years Manami, Kirino and Kyosuke were childhood friends. At this point in time, Kirino saw his big brother as her role model, her hero and her idol. And based on what we saw with the trio slowly growing up, it becomes clear that Kirino is not happy with the way Kyosuke changed over time while he was hanging out with Manami.

That being said after their latest conversation led her to harshly declare that she wasn't his brother anymore and decided to confront Manami over the negative influence she's had over her big brother.

If you've seen most of the episodes so far, Manami is well, helping, normal, always tries to rationalize things and kind overall. But as the old saying goes, all warfare is based on deception and in that paticular episode (ep 13 season 2, I reckon), we see the mask come off for the first time. And all of a sudden, Kirino's aparentely one-sided animosity towards Manami and other girls (including close friends like Ruri) who show any affection towards Kyosuke makes perfect sense.

Sensing a potential rival / obstacle, Manami drops a painfull truth bomb that has enough nasty shrapnel that actually does more harm than good.

When you break it down, what Manami saying isn't wrong: Boys grow up, their attitude changes and of course they want to start hanging out less and less with their youngers siblings, be with more age-appropriate friends and have girlfriends. None of that is a lie. However, the truth bombs stops and the nasty crap starts when she insults her memories by declaring that her perfect little brother never really existed, despite all for her previous experiences.

But here's where Manami gets really nasty, she takes Kirino's confrontation as a signal that she's not only a potential rival but also an obstacle that's in her way. Which is why she twists Kirino's desire to look out for her brother and to be protective of him as presents them to her as though they were romantic feelings ("You know it's actually disgusting for a brother and a sister to have romantic feelings toward one another").

The thing is she's not wrong either on that: incest is bad. But she did so by blurring the lines between sibling affection and sexual/romantic affections so effectively that Kirino is left heartbroken, confused and disgusted.

As a result Kirino hates Manami, hated what her brother had become and anythin' that Kysokue would say or do would be understood as creepy. As a result she strayed as far from him as possible. So for a couple of years, Kyosuke was a complete stranger to her. That also made to seek out some confort in the form of erotic little sister pc games because of the idealized settings (the overprotective and kind big brother who always pleases her sister) and the magical girl animes that she enjoyed as a kid.

Which is why the anime makes a important point about relantionships. Sometimes being a good siblings isn't just about helping each other out it's also protecting them and calling them out on it when they are in a bad relantionship. And how a bad relantionship can harm family. That's exactly the point Kirino was trying to make when she brought over the fake boyfriend. The "fake" boyfriend had to measure up to the sibling's standards and not lead her astray as it sometimes happen. Same with Ruri and Kyosuke's brief romantic relantionship that left our hero in complete shambles. This time Kirino had the knowledge and the maturity to help his brother out. When Ruri and Kirino have their face-off, however, she finally opens up to both Ruri and Kysouke about her feelings towards her big brother. In particular how other girls might have a really bad influence on him based on her disturbing conversation with Manami.

Though in this particular aspect, Kirino does sort of evolve, since it's clear that despite all the oddness, Ruri made his brother happy and Kirino knew Ruri well enough that deep down she knew she wouldn't lead him astray. Which is why she was willing to give up on her long bottled-up romantic feelings towards her brother so he could be happy with another girl.