Let her learn to soothe herself. I like sleeping with my animals, so I sleep with them, but I do crate training during the day. I put her in her crate AFTER exhausting her, and give her something she can chew on if she wants. She screams bloody murder as I step out the door to go feed my horse or go to class, or even just go down the road for a moment, and she's asleep in about 10-15 minutes.
Depending on her age, you might need to take her out during the night... I mean... when you REALLY have to pee, do you want to have to hold it for another 5+ hours? It can be uncomfortable, and while I know I'm not a dog, I would probably whine too. So if possible, see if maybe you can get up around 1 or 2 in the morning (or midnight, or whatever works best), and take her out immediately, and exhaust her for another 10-20 minutes, then put her back in her crate for bed.
And then... don't give in. The ONLY time you take her out of her crate is when she is quiet and calm. She'll eventually associate her being able to come out with being calm and quiet, and she'll be more calm and quiet. At first, if you have time, play crate games and put her in and out really quick based on how quiet she is. And extend the time, and so on. Other crate games are great for teaching HOW she gets to come out, and makes her WANT to go into her crate.
Remember, her crate is her safe place, and she should want to go into it.
And it's OK. Babies cry. If we cater to their ever want and need, they will never learn how to self sooth, and IMO, that's how people end up with dogs with extreme social anxiety, because they never learned how to soothe themselves and be alone.