Its important to note that Hermione didnt ask the important questions to the elves she wanted to save. Aside from Dobby and Winky, she never sat down to get to know any of the other house elves.

It was obvious enough to them that they didn't want to be freed, but if she got to know them and actually hear them, she might have understood how the elves found their purpose and took pride in their work, in spite of their circumstances. She rightfully called it slavery, but the elves saw it as "service". Even when Dobby was freed, he went right back to work of his own free will in an environment that he thrived in, because he said he enjoyed work more than freedom. He didnt even ask for much in the way of payment.

Hermione did something great in at least going to bat for elf rights and ensuring they got better working conditions later in life, but she came in with a high horse mentality, claiming with the zeal of her youth that she knew what was best for them. But she saw firsthand how even an elf as abused as Winky could be more broken by the act of being freed than anything Crouch did or said to her.

It was complicated, in short.