There is really no way to do this except to take her out of the crate. She has been taught that it's acceptable to have bowel movements in her crate and it was her only option for a long time. So, she's going to continue to do so. I would recommend using an x-pen instead of a crate. It's a six paneled cage that you can use indoors. Put puppy pads down in the cage one side and make the other side a living space. Add a bed, food and water and toys to that one side. I bet you will see her go to the other side if she has the option.
We have rescued a lot of puppy mill dogs and this is one of the only ways to break the habit.
After she gets used to the puppy pads, you can then start training her to go outside during the day.
Let me know if you have more questions. I would be happy to discuss this more.