Putting her in a crate overnight is perfectly fine, but just make sure you are getting up to let her do her "business" throughout the night. If she whines, open the crate door, pick her up and take her right outside (or to the pee pad if you are indoor training). Don't let her feet touch the ground until she is at the spot you want her to do her business. Once she's done, put her right back in the crate and go back to sleep. Don't talk to her while she's in the crate or when she whines.
She will eventually get used to it. Our little furbaby got used to his crate overnight pretty quickly and started sleeping through the night after only a week or so. We are grateful for that, as getting up every time he whined started to get old pretty quickly
