You can use the Nova classification[0] which has 4 groupings. First 3 are nutritionally harmless, the fourth is highly processed.
Whey protein vs tofu? One is in your favorite Hunan dish, the other is sold in tubs next to dubious supplements. But, so?
So pies made with lard, sugar, and served with whole-milk ice cream?
Think of risk profiles rather than harm amounts.