The original question was about the maggots spreading diseases. To me that is not a problem, I don't think they will.
Some other things have been mentioned. I don't know why those chickens are dying. If you deal with living animals you also deal with dead animals. That's not always because of disease or mistreatment. I don't know how many chickens you are talking about in that commercial farm, but one of your chores will be to deal with dead bodies. The previous people came up with this way to manage it. You need a plan to deal with dead bodies.
If those chickens are dying from a disease the rest of the flock is already exposed. Many of us don't like to deal with dead animals, I don't either. I don't think the risk of transmitting a disease with that method is all that high with that method.
I agree the smell is probably horrible. Flies may be a real nuisance, there should be a huge population of flies. If that is close to your home flies may make being outside miserable. Something I haven't seen mentioned, I'd have concerns about attracting predators. There are lots of reasons I do not use feeding method that but worrying about the maggots spreading a disease that hasn't already been spread is not one of them.
I don't know what is going on but I think you should have an honest heart to heart discussion with the owner or manager. Find out what is expected of you and let them now what you expect of them. It is very possible you are not a good fit for this position. That's not intended to be a criticism of you, I probably would not be a good fit either.