I think the problem you are outlining seems to be more relevant regarding a socio-cultural phenomenon of "scientism" rather than science as a discipline. Any centralized social institution will degenerate into bureaucratic fiefdom given enough time and money, and modern scientific institutions are no exception to this inevitability. I don't think most scientists believe in scientism; Dr. Richard Dawkins is likely to be a rare exception among his circle.

I agree that scientific method is a tool that is useful for specific questions regarding our environment. Scientific method inductive reasoning, but the publication paradigm that necessitates mathematical statistics favors deductive reasoning. I think scientists do fall into the trap of using mathematical deductive reasoning in formulation of hypothetical postulates and confusing it with inductive scientific method. The multiverse hypothesis is one such example; a postulation that can never be tested, thus is non-inductive in reasoning and not scientific. Yet, how many lay folks think multiverse is a "scientific hypothesis"?

I am reminded of an old video game quote, "Will we next build false gods to rule over us? How proud we have become. And how blind." (Sid Meier's Alpha Centauri). I think some in the lay public has indeed replaced old religion for scientism, but I don't think science itself is the problem.