Apples and oranges here. We have no idea what Walder Frey's character was since they didn't spend any time developing him. Same thing with Joffrey, he killed Ned Stark in Season 1, Episode 9. They hadn't developed the charater enough to know how he would act. But what they did show of him wasn't contrary to anything he did previously. By the time he eventually did die, killing Ned Stark was totally within his character.
Dany on the other hand they spent 7 years of character development. She didn't kill without (in her mind) a noble purpose. Slavers, people who betrayed her, wronged her or wanted her dead. They spent years showing how merciful she could be, how she was able to check even her worst impulses, how she went out of her way to do the right thing. She didn't kill any innocent people. She certainly wouldn't have killed children. When her dragons did, she locked them away. Ever since Tyrion joined up with her every other scene is about "breaking the wheel". If she died, everything was lost and Westeros would be status quo. Why spend years building up to that to have her basically go against everything she's worked towards? It doesn't make sense.