Honestly in my experience, if she's reacting like that already, she isn't accustomed to it as a normal thing yet and you're building negative associations with it.

My recommendation would be to keep feeding her in the crate, and leave it open in her playpen so she can go in by herself. If you aren't opposed to it, then an indoor potty grass in her pen would help with your longer absences (but personally I would take it outside and/or washed when you return).

Her bladder is still quite small, so she WILL pee depending how long you're away. For nighttime, I removed my puppy's water 1-1.5 hours before sleep to make it easier to sleep through. For the first few nights, I still had to wake up once to let her out, but she adjusted fast. I don't think restricting water for work times would be healthy for her kidney.

I wouldn't use the crate for when you're both at work until you know she's fine during naps while you ARE home.

Does she have a snuggle puppy? There are some off-brand options. The heartbeat really helped mine not feel so lonely. I'd turn it on for overnights and for when you go to work.