Okay, so I kind of stole everything out of Gladys' safe. And now every time I go to Groundbreaker, they shoot me on site. But, my reputation with them is Agreeable. So how do I fix this? I've tried leaving and coming back, I've done a few of their quests, but can't turn them in because everyone shoots me when I get off the Unreliable. How do I solve this?

I remember something in the tutorial that you have to leave for a period of time for things to cool of.  I don't recall the exact time frame and I am sure it will be a hassle to have to leave then come back at a later time.