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Before the proof, Marshall and Warren had little more than a suspicion (not enough to topple an accepted theory). Their first H. pilori cultures were in 1982, with little success. Their results of the famous bactery drinking after giving up the culture experiments were published in 1985, only three years later. It's not realistic for a scientist to expect a theory to go away because you have a hunch, even if that hunch turns out to be correct! If anything the Marshall experiment show that in science you can go against the main theories and turn them around if you have proofs.
That's very different that something like "I don't believe in evolution because this sacred book written thousands of years ago says otherwise".
"Settled science" is nothing resembling a homogeneous body of certainty. It's a huge, chaotic mish-mash - of everything from actual rock-solid results, to "it sound reasonable at some point...then human nature took over" baloney. Everybody <cough/>knew<cough/> the latter, so nobody ever carefully checked.
And the worst part? Even long-tenured experts, specializing in the specific scientific niche, seldom know how certain their various facts actually are.
We created the scientific method and now we're basing more and more knowledge on demonstrated facts/truths. Some of the knowledge will be invalidated and removed.
In non-science that doesn't happen. In non-science (religion, flat earth, or whatever domain you want), facts/truths only change when a figure of authority orders the change, but even that is problematic and many practitioners will refuse.
We'll never reach a state where all scientific knowledge is demonstrated. Some parts are currently impossible to demonstrate. And even if we could immediately validate everything we know, some new knowlegde can still invalidate old demonstrated knowledge. See newton mechanics vs. relativity. We use the best science that we have.
That healthy skepticism likely won't cause any paradigm shifts in most cases, of course, but the point here is that is no reason to surrender the skepticism.