She'll be fine in the crate
She's safe in there
How old is she? If you don't want to keep her in the crate, then maybe you can get her an x-pen and put the pad on one side of the pen, and her food, water, and bed on the other side. That way you don't feel like she's being confined. That is if you want her to learn to go potty on pee pads.
Be careful with the collar...If she's a climber, the collar can get stuck on the baby gate. I read a story on here one time that the dog had accidentally hung himself like that..
As far as food goes, you need to make sure she's eating enough. Do you free feed her or do you have scheduled feedings?
You're doing a great job! Don't worry sooo much