The Constitutional requirement on the judge was to handle this case in a strictly secular fashion. That doesn't mean the ACLU can't bandy about charges and so forth, but misbehavior on the part of the board (having "impure thoughts" I think was the charge) does NOT allow the judge to step into the case and commit the same misdeeds.
Think about it ~ just because a serial killer is being tried doesn't give the judge the authority to gun him down as well as the jury and people in attendance.
There are legal standards of a strictly secular nature that must be used in these sorts of cases ~ ACLU proposed shortcuts are merely more of the same sort of garbage we thought we'd put behind us in the Enlightenment.
It was the school board that started this silliness, not the ACLU or anyone else. You want the state to remain secular, as do I. The Dover school board needed to take creationism and teach it in philosophy class where a)it belongs, and b) I would support it 100%.
I've long been of the mind that in order to really understand western culture and western history, you should be well versed in western religious thinking.