No, what makes it OK is that it works. Science does progress. In fact, I don't know how science can progress, beyond the first rudiments, without having working models to refer to. You can claim all you want that evolution is bunk, but you aren't nearly in a position to say the same about chemistry and physics. Since they all use the same philosophical approach, obviously that approach is not the problem.
In my field of particle physics, for example, the working model is called the Standard Model of Particle Physics. The problem with it is that, even though it accounts for more natural phenomena--and to a greater degree of accuracy--than any other theory in science, and even though we have no generally accepted experimental results that contradict it, we already know it to be wrong. At about the 1 TeV level (or before), it mathematically has to fail. Even so, we refer all experimental results to this model, because without some conceptual framework there'd be no way to make heads or tails of the experimental data. Science is more than a mere list of facts.
As for the comparison between the working model of biology (evolution) and the working theory of chemistry (the atomic theory of matter), I can think of at least two experiments where the atomic theory of matter falls flat on its face, but none for evolution.