I can discern between astronomy / astrology - so did the judge.
I can discern between scientific method / IDcreationism - so did the judge.
Ok, the decision is based on the religious nature of Intelligent Design, nothing more:
we conclude that the religious nature of ID [intelligent design] would be readily apparent to an objective observer, adult or child (p.24). In that vein, the writings of leading ID proponents reveal that the designer postulated by their argument is the God of Christianity (p, 26), ID is nothing less than the progeny of creationism (p. 31). Establishment Clause forbids not just 'teaching' religion (p. 46, footnote 7).
Bottom line:
Accordingly, we find that the secular purposes claimed by the Board amount to a pretext for the Board's real purpose, which was to promote religion in the public school classroom, in violation of the Establishment Clause. (page 132)
Conclusion:
The proper application of both the endorsement and Lemon tests to the facts of this case makes it abundantly clear that the Board's ID Policy violates the Establishment Clause. In making this determination, we have addressed the seminal question of whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents.
It's out because it's religious and therefore is barred by the Lemon test and the Establishment Clause. Part of the argument was that since the Scientific Revolution science has been limited to exclusively naturalistic causes, thus is fails as science in that sense.
Personally I have never advocated teaching creationism in the public schools, secular institutions are simply an absurd vehicle for such a thing. The decision said one thing that is not true now, Behe did publish an Intelligent Design paper on gene duplication not that it really matters that much:
ID has failed to gain acceptance in the scientific community, it has not generated peer-reviewed publications, nor has it been the subject of testing and research.
The decision was predictable, perfectly proper and has nothing to do with whether or not God is Creator. It has to do with whether or not Creationism and Intelligent Design are religious and of course they are profoundly religious. Not being scientific or naturalistic doesn't mean something isn't true.
Have a nice day

Mark