Judge Jones acted in the best conservative tradition. He carefully determined the facts, which are pretty much beyond dispute: Here's the judge's opinion.
Having found that ID is creationism, he then applied precedents (he didn't make up his own law) and ruled that it was unconstitutional to present a religious doctrine in a science class. Not a difficult decision, when you're following the law.
Apparently,. some on the right actually want judicial activism, provided it benefits their agenda.
Judges are not in business either to decide what is good and bad science or to decide what is good and bad theology.
He was appointed by Bush? So what? Earl Warren was a Republican appointee. David Souter was a Republican appointee. They have both made more trouble than the worst Democrat judges.
Evidently Bush made a mistake. He never should have appointed this activist friend of the ACLU.
His finding that ID grew out of fundamentalism, that it is a form of creationism, and that evolution is no contradiction to anyone's religious faith are all personal opinions. At least two of them can only be the judge's personal religious convictions, and the other is an erroneous historical opinion.
The author of this article sees far more clearly than this judge.