I think what you are pointing out isn't a failure in the educational system, but it is how people treat the 'quest for truth' in their lives. I am not quite sure how this passion became instilled in me, but at some point I wanted to know the facts. I didn't care what people believed, I wanted to know *why* they believed it and whether I could believe it myself.
What I like about you is that you also have this quest for truth. As Richard Feynman once said, 'the easiest person to fool is yourself'. And if there is any quote that stands out in the history of humanity, that's got to be on the top 10.
So, if you want to just accept what teachers, politician, ministers, and even philosophers, mathematicians, and scientists, then you are doomed at some time to fall into a situation where you are dupped. Of course we all can't become general relativists, quantum mechanical theorists, QED theorists, philosophers of epistemology, philosophers of science, etc. However, I think we can learn which institutions are 'safe bets' from ones that aren't. Those who believe only science is a 'safe bet' (someone such as yourself?) I have found to be naively in error. Scientists are geniunely very poor at correct interpretation of scientific theory and are lousy philosophers (for the most part). Philosophers, on the other hand, have to be watched carefully otherwise you could unwittedly tackle subjects that are really scientific subjects of the 22nd century (or some later scientific discipline). I'm reminded of the philosophy of mind which has considerable discussion, but I'm skeptical whether some of this inquiry is needless given the strong possibility (in my mind, anyway) that science will someday make more progress when that time comes. I'm not discrediting the philosophy of mind, I'm only saying that it is better to forego some discussions for a future period when the speculative comments of today can be empirical based. Of course, much of philosophy is not in that genre so I have high confidence that philosophy is the best method of inquiry for many of those mysteries.
Hence, to truly avoid the pitfalls that you mentioned it isn't good enough to have a high expertise in science. You must have an expertise in other fields of study, but more importantly you must have a drive for honesty and truth which can only guide one in their approach to the tough questions.
Warm regards, Harv