I mean what is important is that Shino is happy and has a wonderfully cute little girl, Kyouya being the father is not necessary.
You can argue that the little girl would not be the same exactly and that it is sad.
But if we follow the Steins;gate idea of worldline, they all exist parallel to each other but we only experience one at a time.
So she is not erased, it's that Kyouya would not be in a worldline where she exists as his daughter.