"Let instinct trump logic" - bad advice. Instinct is simply pattern matching current conditions against memory. Without experience, instinct is a poor criteria and logic should be employed. Read Kahneman for the supporting research into that.
I'd also recommend Jonathan Haidt's The Righteous Mind (http://www.amazon.com/The-Righteous-Mind-Politics-Religion/d...). He makes a lot of interesting points, including that most people come to a conclusion about an issue, then look for reasoning to support it, and that most of us operate on instinct most of the time—logic is a more costly, difficult mode whose use can be cultivated but which is not at all the default.
Not to say instinct is bad. It's extremely valuable, and as Blink Theory pointed out so famously, has it's place as well.
But as you said, I agree it's bad advice to let one simply trump the other.
However, there have been billions of bad-instinct decisions as well, ranging from "should have zigged instead of zagged" while driving a fast car around a curve to Napoleon invading Russia.
But, if instinct trumped logic as the author suggests, humans wouldn't be at the top of the food chain and driving cars.