It's totally reasonable that your gf is uncomfortable with this. Having your ex move to your city and become your coworker whom you would presumably see every day means you'll be re-negotiating your relationship with her. Ideally into something respectful and professional, but it's going to be a transition and everyone is going to notice it.

You don't mention how your divorce and subsequent co-parenting/ex relationship went or is going, how long ago the ex became the ex, and/or whether it's likely your ex is going to do anything to try and re-stake her claim in your life or cause drama. Unless your industry is very small, it's kind of telling that she would apply to your small/mid-size company of all the potential options she might otherwise pursue. Basically... are you the reason she's applying/moving? This could be a lovely thing for the kids' sake if you are both maturely moving on, or it could be stalker behaviour that you seem to be encouraging.

If I were in your girlfriend's shoes, I would be wary too, but depending on the circumstances, hopefully you can either put her at ease, or you need to do what's best for you and the kids as opposed to the girlfriend. Dating after divorce is hard.