Part of the issue is in educating consumers about the dye and that removing it makes no difference to the food.
As a child I remember a brand of processed peas I enjoyed. As you'd expect from peas they were green. Not the kind of green you'd expect from peas, a much bolder green. Then they took the coloring out and the peas went from being a chemically enhanced green to, well, the kind of green you'd expect if you cooked peas and put them in a can. I didn't like the look of them and from what I recall from my parents' comments there were many customers who didn't like the look of them. Because, you know, peas are green and not this muted color.
Colors in candy have caused issues with making kids hyperactive for decades, and yet still we use them. You'd almost be forgiven for thinking there's extra profit to be made in keeping people unhealthy.