The biggest mistake of the episode was having Shae come at Tyrion with the knife and Tyrion killing her in self defense. I'm really not even sure what they were trying to do with that scene. Unlike the books, show-Shae is for the most part portrayed her as genuinely loving Tyrion. She refused diamonds and wealth in the free cities, got all pissy that she was going to have to share Tyrion with Sansa, and cried her eyes out when he attempted to send her away (Tyrion wasn't even in the room, so they weren't fake).
The testimony was set up as a combination of woman scorned ("I am a whore, remember") and pressure from Tywin/Cersei in rigging the trial (the point of the subplots of Cersei finding out about it and Tywin ordering that she be sent to his chambers). Her being with Tywin is easily explained by his own fucked up personality and hypocrisy. But then in the last scene, it's like they decided to toss out all of that characterization and put Shae right back into her book-version of not giving a shit about Tyrion. She comes at him with a knife immediately and doesn't even attempt to talk him down. He kills her in self defense, and that's that. He's sorry he had to do it, but it's not like he had a lot of options and he's really mad at Tywin for shattering his illusion rather than anything Shae did.
What they should have done was have her plead for her life and try to explain that the situation wasn't her doing. Throw in some talk about how he was right, its not safe in King's Landing, and she realizes now how dangerous Tywin and Cersei are. He is heartbroken and beyond reason though, so he doesn't listen/believe her and chokes her out. She doesn't put up a fight. As the rage subsides he painfully realizes that she may have been telling the truth (say he notices some marks of abuse via Tywin) which causes him even deeper psychological trauma. He goes to confront Tywin, who dismisses her as just another disposable whore. Tyrion arrows him, but falls into the deep depression he finds himself in during book 5. Shae successfully replaces Tysha in Tyrion's psyche and the story goes on largely unchanged.
But that all hinges on Shae actually being genuinely in love with Tyrion, like Tysha was. The knife ruins that and really skews his whole characterization going forward. But I guess Tyrion is the show's golden boy and can't do anything that is even remotely morally questionable. I'm sure next season they will neglect to include his melancholy/contemplating suicide and will skip to him making japes at Jorah for being in the friend-zone in short order.