Crate training a rescue puppy

Hi everyone, I just adopted a 7 month old shepherd mix. My understanding is she was an owner surrender at about 4 months and she was on the euthanasia list due to overcrowding + her high stress in the kennel until a rescue stepped in last minute. We JUST brought her home Saturday, so we are going through a decompression period where we are introducing her slowly to new things and even rooms in our house, with no outside people or places. Shes very shy but has opened up so much already! Shes a great listener too, and she’s crate trained. I’ve been putting her in the crate periodically for naps, occasionally for meals to keep it as a positive place, and when we sleep at night. She maybe cries for 1-2 minutes and then settles.

My work office is upstairs and we haven’t introduced her to that floor yet, she’s scared of how many steps there are, and we are taking it slow. So when I “go” to work she’s been hanging out with my boyfriend because we haven’t had overlapping work hours yet, but we will soon. Today was the first day we attempted to leave her “alone” in the sense that my boyfriend crated her to go to the store and I was upstairs on meetings. She would not settle and was frantically crying for about 30 minutes. I felt terrible because I couldn’t step away to go check on her. She had to of been crying loud for me to hear her all the way upstairs too. After my meeting I came and let her out of her crate, she was thrashing around (but may have only started that when she saw me, I’m unclear) and took her outside just in case it was a potty situation but it wasn’t. She was stressed and jumping on me. I got her settled down by redirecting her energy into playing fetch. Luckily I was able to finish my work day downstairs, so I didn’t have to crate her again.

I’m struggling with how to handle this. I understand the importance of crate training, and my goal is to keep her crate trained and use the crate when we aren’t home, for sleeping, naps, when we need her to stay safe in a spot, etc, so it’s not like I plan to only put her in there when we aren’t here. But it seems to be when she becomes distressed. Equally I know it’s bad for her to never be left alone. This is going to naturally be difficult because I do work from home, but my hope was crating her could give her some independence from me during the day too. But it really broke my heart to hear her cry like that, I just kept thinking that she must be so scared from her experience in the kennel. I’m so scared of doing this wrong and making her associate the kennel with something negative, her developing anxiety, or worse, reactivity. My previous dog was reactive and although she will always be my soul baby and mean the world to me, I would be lying if I didn’t say it was also equally exhausting and I really am probably overly nervous about going down that path again, so I want to get this right. How can I get her comfortable in the crate alone – is it cruel to do so given her background?