>The slogan that "the Catholic Church" did this and that is popular in certain circles. But it collapses at the slightest examination.

What makes you think that? From http://abob.libs.uga.edu/bobk/whitec03.html
"This was on the 26th of February, 1616. About a fortnight later the Congregation of the Index, moved thereto, as the letters and documents now brought to light show, by Pope Paul, V solemnly rendered a decree that '_the doctrine of the double motion of the earth about its axis and about the sun is false, and entirely contrary to Holy Scripture_'"

>First, the reported behavior predates the concept of multiple European christian sects, each of which is just as much a descendent of that original European church.

That irrelevant, but since you brought it up:
1054: Great Schism creates Orthodox and Roman Catholic Churches http://en.wikipedia.org/wiki/Eastern_Orthodox
1308: Protestant Reformation Begins: http://en.wikipedia.org/wiki/Protestant_Reformation
1560-1689: Reformed churches begin http://en.wikipedia.org/wiki/Reformed_churches
1616: Inquistion of Galileo http://en.wikipedia.org/wiki/Galileo

In otherwords, yes the Orthodox and Protestant churches existed and yes it was the Catholic church.

>Second, it dates to a time when the church wielded great secular power and exhibited the behavior of the powerful.

If you mean political and governmental power, yes I agree.

> Trying to assign that sort of behavior to religion is a demonstrable failure. I gave examples.

It wasn't the Mayor of Rome that pursued him, it was Paul V followed by Pope Urban VIII.

> Third, every institution has skeletons in its closet.

I'm not arguing that, instead I'm arguing that only after the power of the organized religion started to decline were thinkers allowed to pursure knowledge with less hinderance.