Well, basically you're wrong.
Alas, it does not appear the School Board was neutral. They on numerous occasions made clear their goal was positively to introduce religion into the classroom. The recent Ten Commandments cases make it clear that the objective of the government action is paramount in deciding whether the actions are constitutionally permissible. This is why the ACLU made such an issue of the discussion of religion in the school board meetings, and why the Thomas More lawyers have been trying (unsuccessfully) to keep that evidence out.
This commentary puts you squarely on the side of the thought crime advocates. The two cases are not analogous, the Ten Commandments case involved action the Dover case according involves only thoughts because the actions of the school board do not reflect the thoughts you have assigned to them.
More to the point, you seem to think that federal judges sticking their noses in where they don't belong will somehow advance your particular agenda. History tells us you are wrong. The history of judicial activism is quite clear, it poisons the well and flames the culture wars.
You can not win a culture war, the numbers are not on your side. You can advance science by muzzling people like Dawkins and explaining that science and religion are not incompatible but if you think you can use the federal courts to accomplish your goal you are sadly mistaken.
Finally, I am simply arguing the facts of this particular case. Nothing in the constitution or the original intent thereof requires neutrality. In fact, US history contemporaneous with the ratification of the first amendment would directly conflict with the notion that government, especially local government, can not advance religion in general. And that was the law until 1940 and Everson.
You look at Dover with glee because the ACLU and some small number of parents have managed to make a federal case out of a short four paragraph statement that in no way, shape or form advances anything. I look at your glee and shake my head at the penchant of people to misuse power when that power can be used to advance an ideology.
I'm analyzing the case on its legal merits. jwalsh07 accuses me of 'glee' at the result, all the while claiming that the case against the school board amounts to 'thoughtcrime'. Bit of a disconnect there. Yes, as a parent of public school kids, I do want my children taught biology and not superstitious nonsense. I'd prefer to handle the issue locally and democratically, as we have successfully done here in Nebraska. Do I approve of a federal lawsuit as a last ditch alternative? Probably; I think the establishment clause is important, and ultimately, since its in the US constitution, there has to be some recourse through the federal courts. And I certainly take glee in theocrats making a pigs ear of the case.
Of course, if we were discussing a different case, say the case of the student who sued his instructor at Texas Tech because the instructor would not write letters of recommendation for creationists, the sides would be reversed. In that case, intrusion of federal judges to protect the religious rights of a state university student would be entirely proper, and I'd be defending his individual right to write recommendations for whatever reasons he wanted.
Yes, it's a culture war, and it's one that neither side is fighting with any particular set of consistent jurisprudential principles. So those of us on our high horses should dismount before we get thrown off and break something :-)