Yes, he can be treated, but of course it will be difficult to get his cooperation. I would start by getting all the "bad" foods out of the house. Period. Don't allow anything like that near him. Explain to well-meaning persons that may undermine a healthy Diet that just like a child with diabetes, he may not have any Sugar at this time. Provide acceptable snacks when he goes to daycare, relatives, etc.
Next, I would try providing a candida-unfriendly environment all around. For example, adding eucalyptus to his bath, choosing a shampoo with tee-tree oil, etc.
Start using garlic in your cooking- everything that can take it. Then start "practicing" swallowing tiny "pills" i.e., could be a very, very small piece of carrot, and you have him drink it down. Start with very tiny pieces, and make a big deal of it, with cheers and "hoorays." Slowly make the pieces a tiny bit bigger, until he would be able to swallow a gelatin capsule. Then, you could get a prescription for him, and put the nystatin in a gelatin capsule.
I completely understand the reluctance to treat your son with homeopathy. Much better if you can get a cooperative doctor to help with dosages, etc.
From your description, it does sound like there is a possible fungal problem. Heck, if I could go back in time, I would also use a lot of Vicks Vapo-rub. It is the only thing that cleared up the fungi on my nails, and maybe it would have spared my children a lot of grief- breathing the vapors may have helped a lot.
By the way, when my son was a toddler he showed no strong preference for sweet foods, though he liked them. In fact, that summer when he was hungry, he wouldn't even ask to go in for a snack. He'd just walk over to the garden and help himself. I have a very funny memory of looking over and seeing him bent over a broccoli plant, chewing away! hee... He was not nearly as affected as my daughter, who has had major life-long problems from it, it seems. As hard as it is to get a toddler's cooperation, it will only be more difficult when he's a teenager.... :)
Get rid of the problem now, you'll be so glad you did.
I also used to be plagued by allergies, but they all went away as my candida problem improved. Other inflammatory problems also cleared up.