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.
Note added in proof: I can think of one for evolution.
Yes science does work. The problem with your argument is that paleontology is not science and it certainly cannot prove descent.
If you were to let a hundred paleontologists loose in a cemetery, take away the gravestones and ask them to show from the cadavers who descended from who, they would be totally unable to do it even though the specimens they would have at hand are almost perfect and much much better than what they base their extravagant claims of descent on.