First of all, while a private hechsher certainly has a disadvantage and a greater challenge to remain objective, it would seem to me extreme to say that one that has built up a sterling reputation of many years cannot be trusted. Even a large established organization needs a lot of yiras shomayim to admit when they make a mistake, because the most valuable asset to a hechsher is its reputation.
Regarding your question, "blindly holding the highest standards" would require passing on the added cost to the consumer, and the organization must make a judgment call which standards are important enough to demand and which are extra chumros. Also, we live in teva, nature, and an individual or organization must take reasonable precautions as part of the obligation of hishtadlus. Furthermore bitachon and yiras shomayim are challenges that require a lifetime of work to achieve, inevitably not all of us are holding on the same sublime level. While wrong, it would only be human nature if occasionally even the director of a hechsher would make an incorrect decision due to financial pressure, just like each of us inevitably does on occasion. As your Rav pointed out, this would be less likely to occur when there is a Beis Din or other higher administration that the Rav HaMachshir must justify his decisions to.