While what Saki did was evil and awful...I really hate how Karai went from, "Shredder is my father!" to "Shredder is NOT my real dad and I hate him!" upon learning the truth.
For all that Saki did wrong, he did raise Karai. He was as much of a father to her as Splinter was to the Turtles. It doesn't excuse or mitigate the kidnapping and murder, but for 15 years of her life, he was her father, trained her not only to protect herself but to run his empire.
I would have liked it if Karai had been ambivalent, then Shredder actually turned against her, saying she was too much like her real father, and that she come to terms that she could not save him. Or, if Karai had been ambivalent, and Shredder still have been possessive and controlling of her and she come to the understanding that she was as much of Sherdder's child as Splinter's and acted as a bridge between the two. But for her to completely and permanently reject Shredder and side with the Turtles was just a reversal of what Shredder did when he found out the truth about his heritage; and unlike him she never did reveal the truth and still tried to lead the Foot as Karai, not Miwa. Basically, she out-villained the villain. But it's okay because she got mutated (although Shredder did what he could to try to restore her, if for all the wrong reasons) and because she's a "good girl" now.
No, Karai shouldn't worship the ground Shredder walks on, but for her to show absolutely no attachment for a man who raised her is not just unrealistic, but it's a cheap easy reaction to change a character's allegiance without doing the actual work.