I agree there’s a problem with over-analyzing and living in your head, like a Woody Allen character. However, there’s an ambiguity in interpreting philosophical texts as “limited, small, and helpless.” Either naturalistic (analytic, science-centered) philosophy comes off that way because it’s missing the reality of spirituality, as you’d say, or it’s natural reality that seems horrifically limited compared to the spiritualist’s fantasies, and philosophy is only the messenger bearing bad news. So you’re begging the question at issue.
The big question is whether we trust science or our gut as the deepest source of information. Cognitive scientists tell us how our intuitions (heuristics) evolved and help us in desperate situations but also lead us astray with a host of fallacies we’re liable to commit. We’ve completely changed our environment by replacing the wilderness with civilization, so our natural, most comforting cognitive and behavioural habits seem anachronistic and out-of-touch with our new reality. That reality includes the scientific picture of the world, which seeks to naturalize everything.
I agree, though, with Wilfrid Sellars and with what I assume is your view too, that there’s an unbridgeable gap between that scientific image of our nature and the manifest, folk, or intuitive one. Philosophers try to bridge that gap with types of dualism or with more extreme, eliminativist arguments.
I take a pragmatic view of these “images” of our nature (as Sellars called them). They’re models which are more or less useful in different circumstances. The utility of science is obvious. The spiritual model has some utility in regulating society, but that’s a mixed bag. See, for example, the 9/11 terrorists and the various cults and New Age frauds that prey on our gullibility. So I prefer a more philosophical second model that’s not so at odds with science.