My theory is that Alice had no choice but to make this decision, and might've been right to do that
However, by sacrificing the witches, they lost control of the humans who were until now treated as inferior species
After that, the roles reversed, and the witches became the prey, and history was arranged
However, by doing that, they are destroying their own future, since now the witches are sacrifices for stuff they don't even know about, nor even care probably, so they have every right to be angry, especially since they are hunted
Also, as other comments said, the witch hunt became too big, and now they lose witches because they get killed by humans instead of being sacrified to make super soldiers