This is an interesting issue. I've been battling with it ever since I started taking a serious interest in the effect of the food I eat on my health. More recently, I've become increasingly aware of the importance of other factors such as controlling stress (and now the nocebo effect), on health and so have made an effort to reduce unnecessary stress as much as possible.
The result is that I live in a delicate balance of worry/perfectionism vs. a more lax and accepting attitude. In other words, I tend to oscillate between periods where the negative (i.e. worry) predominates, and others where I decide I've been fretting too much and I should relax and enjoy. So there are times where I'm more careful with the things I eat and buy (no factory chicken, remove fat from non-grassfed meat, no nuts, no fruit whatsoever, no chocolate, etc.), followed by times where I let myself drift towards whatever feels good or whatever I can afford, with minimal guilt. After a few weeks the guilt increases and I tighten up again, and so on. Always within a paleo framework, though.
The placebo effect is widely accepted as being a real phenomenon, so I don't see why the nocebo effect would be any less significant.
I am pretty convinced that our mental attitudes and expectations can directly affect our physical wellbeing. Stress can definitely make you ill, whether the source is your negative bank balance or the fact that you just ate a piece of farmed salmon laced with sugary soy sauce. If the physical effect is strong enough, it could cancel any positive effects you might otherwise be getting from an even moderately healthy diet. Most likely this effect varies hugely between people and depending on circumstances, making it impossible to predict.
In summary, my philosophy is: avoid danger to a reasonable extent, but once it's done don't fret about it. Just learn from it, make the best of it and move on. Damage control. It's all about the balance. Maximise the positive (make reasonable efforts to eat the healthiest diet you can), minimise the negative (don't worry yourself sick about the bits that you can't control or the occasional mistakes you make).