I think this is a classic case of intolerance breeding intolerance.
The way I see it, Miss Ahlquist was unable to tolerate the presence of what is to an outside, non-partisan observer, a fairly harmless and benign piece of Christian iconography, and asked it be removed on the grounds of the constitutional division of church and state.
In so doing she created a political, ideological, and theological flashpoint that drew people in on both sides of the debate. Naturally the most dogmatic and intolerant of challenge to their chosen ideology were in the front-row, thereby expanding and deepening the conflict.
My view is that there are no "winners" in such a pointless conflict, nothing has been gained and whole load of enmity has been stirred up. Its a net loss for that community, and especially for Miss Ahlquist.
Its an empty victory because all that's been accomplished is a clearer delineation of battle-lines on ideological grounds. An open display of Atheism or non-Christian belief is going to be no more welcome in that school/community than it was before, in fact I suspect it'll be greeted with more hostility.
This is because belief is more than some words written on a wall, its something that people carry with them. As an Atheist Miss Ahlquist should realise that the ABSENCE of something can carry as much weight as its presence, should the prayer be removed or altered it will stand as a lasting reminder of a deep schism for years to come.