I did a little reading about this during research for this question: What skin colour would living permanently on the moon select for?
Although the research on radiotrophic fungus is in its infancy, it does suggest that it's the presence of melanin in these fungi that gives them their radiotrophic ability. Similar to how melanin protects from UV light, the breakdown of melanin in these fungi via other forms of radiation provides them with energy: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677413/ and https://www.news-medical.net/amp/news/20110824/Melanin-also-protects-from-ionizing-radiation.aspx
The conclusion we came to in my question was that a possibly effective way evolution could protect against radiation exposure would be to ramp up melanin production. So, give your workers as dark a skin colour as you can possibly get (or just employ people of really dark skin colour which is simpler).
The bit where your genetic engineering might come in useful is that gamma radiation is far more penetrative than UV radiation. Melanised skin is effective against UV radiation because it stops there, whereas gamma will quite happily pass through your body and out the other side causing damage the whole way through. So, the conclusion we came to is that melanism throughout the body's organs would be beneficial. So black muscles, black bones, black organs. Melanise the lot!
You could also probably do something neat with radiotrophic fungi providing some energy if you like (engineer the appendix to contain a symbiotic colony perhaps), but if you want protection just cut out the middle-man and melanise.
I would definitely suggest lowering the radiation dose they're exposed to. I sincerely doubt they'd survive 50,000 grays over any extended period of time regardless of their adaptations.