Welcome and congrats on your new puppy!
7 weeks is very young to be away from the litter. Usually 8 weeks is the youngest suggested time for pups to be taken away from mom and siblings because they are still learning a lot of socialization skills.
You may want to really work on socialization with healthy, safe dogs who are UTD on their shots because of this for the next few months. Socialization is so important.
She is not being defiant at all.
She is the equivalent of a 6 mo. old human who doesn't like being left alone. A few things you can do to help, especially considering her age. Is there a reason you aren't crate training? The nice thing about crate training is that you can bring the crate in your room at night. With a puppy so young, when she cries at night, you can put your hand down to the crate to let her smell your hand to reassure her (assuming she's not crying because she needs to potty). This would require more management though, because you will need to take her out to potty frequently. Here is our crate training FAQ: https://www.dogforum.com/dog-training...ning-faq-3974/
. If you don't want to crate train, you can use the same tips on the FAQ only apply it to the xpen you are using. Here is a good video on the topic as well:
Are you planning on having her go on pads for the rest of her life? If not, it can be more difficult to pad train, and then switch to potty training outside (think of an adult dog who uses newspapers or magazines to pee on inside). I would suggest starting with whatever training you want to stay with. Dogs and puppies will typically eliminate away from their sleeping/eating area, but that is it. I'm guessing the first day when she went on the pads was by chance. Here is our potty training sticky that outlines how to train your dog or puppy on where you want them to go: https://www.dogforum.com/housebreakin...-how-tos-2135/
. And here is a video (I highly suggest watching kikopup;s videos; she has training suggestions for just about everything):
The basic idea is management and reward. So take her to her potty spot often (every 20 minutes for a puppy, and after naps/eating/playing), wait 5-10 minutes, then reward heavily when she goes (praise and treats). Keeping her tethered to you or sectioning off your house is the easiest way to keep an eye on her during this phase, then crating her or using the xpen (like you are doing) when you can't keep an eye on her.
Lastly, puppies can only hold their bladders in hours their age in months +1. So at 7 weeks, your puppy can hold it about 2 hours at the very most. That's not saying she will hold it that long. Puppies eliminate all the time: after eating, drinking, playing hard, excitement, a nap, etc. But a puppy also needs to go at night every 2 hours as well.