I suspect processed foods are not harmful. A raw food diet is a lot likely to be less optimal (basically, cooking - which is processing food - is what made us human: processing our food allowed us to break it down a bit meaning a simpler, more efficient digestive process, allowing us to have larger brains).
If you cook from fresh ingredients, guess what you're still eating processed food. Just because the food processing happened in your home, doesn't mean it's not processed food. It doesn't matter where the processing occurred - in your home, in a factory, or wherever, so long as the food doesn't contain excessive quantities of crap. I think the real answer is avoid crap foods. Foods with large quantities of refined sugar for example. I think the main things of home cooking (processed foods processed in your home) is that you know what went into the process so it's easier to avoid the crap simply by not adding it to the recipe.