That is a tough situation to be in. I do not, however think all hope is lost. If you are good to your feet the rest of the time, you should be able to keep most problems at bay. Here are my thoughts, in no particular order:

• Make sure your work boots are a good size. Wear a size that enables your feet as much breathing room as possible without being unsafe.
• Be barefoot/minimalist the rest of the time.
• I am not sure how the toebox is on your work boots, but if it is restrictive, you might want to consider getting a pair of Correct Toes to use at the end of the day. They will help re-habilitate your toes from an overly-restrictive toebox.
• When you are not working, you need to do activity that works your feet. If your feet are not getting developed during the workday, then you should find ways to develop and maintain them outside of work. Walking, hiking, running, on varied/rough terrain are examples of things you might do.
• You might want to consider getting a pair of Barefoot Science insoles to use in your work boots. They are a foot strengthening insole that would enable you to build some of your barefoot muscles while wearing your boots.

That is all I can think of for now. If I come-up with any more ideas, I will be sure to post them here.