Hi Shivani,
if the sugar levels are under control, the diabetic is allowed to eat all varieties of foods in limitations. but on a general term if you have to compare wheat and jowar , then my preference goes to whole wheat flour,as the glycemic index of wheat ( around 50) is less when compared to jowar (around 75). also whole wheat flour has more amount of fiber when compared to jowar, and hence the benefit being that it does not raise the blood sugar as much a jowar does, but also the fiber helps in lowering the over all blood sugar levels of the person.
nevertheless, i dont believe in the idea of a diabetic person completely giving up on any particular food, whether jowar or anything else , but the key behind their blood sugar problem is limitating the quantity of food and not going over board with any food whether wheat or any other .