A member of my shul, scientist who was on the short-list to win a Nobel a couple of years ago, made an interesting point about his own ethical issue. As a scientist involved in biology, professionally, he must assume the existence of biological evolution, and this conclusion is apparent in the papers he writes which discuss how cell biology and behavior evolve over an observable amount of time. On the other hand, he religiously believes that the Torah's account of creation is the truth, although perhaps not literal in all respects. He wonders whether by adopting as true previous science concerning evolutionary biological development, his work directly conflicts with Judaism's fundamental tenets. He has his own rationale, but are there responsas that address this issue for scientists? I note that there have been some pretty amazing rabbinic scholars who were also scientists, Rabbi Aryeh Kaplan (a physicist), for one. So I would imagine there must be something. Among the issues I wonder about is whether the rabbis would consider this scientists' representations as being ganeives daas (improper deception).
Torah and religion teach of the world as it is (assuming that we know to understand the teaching correctly) while science deals with the world as we see it. There cannot be any religious problem to speak of the world as God has shown it to us, as long as we recognize that our perception of the world should not be taken as the ultimate true description of the world. (As an aside, this is something which should also be recognized from a purely secular viewpoint.)
Therefore, a religious scientist should not have any problem professionally speaking of the world as it is seen from a scientific perspective, while personally believing that that is not actually the true account of reality.