That makes it indoctrination of dogma, not science despite the reverence paid to Saint Darwin.
And you still haven't said how having a federal judge dictate to a local school board what is or is not religion in a local somehow is acceptable under the rubric “limited government”.
Judges need to enforce the limitations of government when those bounds are exceeded. Ruling that religious doctrine cannot be taught (and ruling that I.D. is a religious doctrine) is perfectly compatible with limited government.
Government deciding what religious precepts are correct and teaching religious belief and particular scriptural interpretations, at any level, is incompatible with the nation of religious liberty our founders envisioned.