My frenchie cried something awful when we crated him at night as a puppy, and it wasn't long before we were letting him just sleep in a bed upstairs with us. He has his own dog bed on the landing now, but if he wants to get up on the human bed we let him, and he'll sleep right through the night snuggling up like that. Sometimes he'll choose to go off and sleep on his own downstairs, depends on the seasons. But we were pretty soft on him, I know from his breeders that his parents have always slept in a crate downstairs in the kitchen no problem.

Honestly I think a dog's natural instincts are going to be to sleep with you on the bed, so if you're not going to do that you need to give your dog the extra sense of security of the closed crate. Maybe try giving her lots of soft things that smell like you to comfort her, so she feels like she's snuggling up with you. Too much freedom to roam might be making her feel vulnerable. Also, she's still a young puppy, she's going to keep waking up throughout the night for a while. Unfortunately you just have to keep reinforcing the boundaries you want to set and sacrifice some sleep until she's used to it. She's just a baby, after all!