You have a cuddler on your hands. She is crying because she wants to sleep with you. If you are exercising her that much and she is getting enough food through the day there is no reason for her to have to go potty in the night except on rare occasions when she drinks a lot. Feeding her in the middle of the night will make her have to go again soon though.
Don't feed her after her evening meal. Walk her before bed and make sure she does her business and then let her stay in her bed through the night. She knows you are going to let her get in bed with you eventually and that is what she really wants.
Gracie has slept with me from night one so I'm used to her letting me share her bed with me.
She has her own pillow and blanket which she starts out with but usually by morning she is ether snuggled up against me or actually asks to get under the blanket. She is a heat seeker.
Dogs are animals that are used to sleeping on top of each other. They grow up that way. Some Yorkies tend to get cold easily. (Gracie was upset when I turned on the AC or a fan this summer) I had to get her winter pajamas out for her.
Maybe a softer bed with a warmer blanket would help get your dog used to sleeping through the night. As it is you have set up a pattern that is hard to break. If you don't want her to sleep with you then you are going to have to endure some crying until she accepts that you are not giving in to her cries.
I have had dogs in my bed since I was a kid so this is no new thing to me. I know some pet owners don't like to share thier bed's though. I hope you can work out a solution.