Depending on who you listen to, the withdrawal of the European Commission candidates in the face of the Parliament's refusal to support them was either a shameful left-wing assault on religion (the Times went so far as to use the phrase "witch burning" yesterday) or "the birth of parliamentary democracy" in the EU. There are a couple of points that stand out to me.
The first is that the row about Buttiglione obscures the real concerns the Parliament had with some of the other commissioners. They also rejected Neelie Kroes, an impeccably liberal Dutch businesswoman, on the grounds that she was in a conflict of interest as Competition Commissioner. Looking through the list of her former directorships it's hard to disagree - practically every Dutch and quite a few other companies of substance are there. They also rejected the Latvian Ingrida Urbe as Taxation Commissioner. She is a Green, but a Eurosceptic Green, and they were dissatisfied with her statements about her own finances. They also threw back a Socialist, Laszlo Kovacs, who was proposed as Energy commissioner, on the grounds that he wasn't up to the job. In fact, the Parliament's ire seems to have been very fairly distributed across Europe - here goes a southern, Catholic conservative! Followed swiftly by a Protestant, northern economic liberal! Thrown out chiefly by the Liberal group! And a Baltic Green! And a Central European Socialist!
This kind of equal opportunity castigation is just what a parliament should look like. Appointments should never be made because they represent a constituency or faction. Neither should they be unmade. Instead, the parliament should be united in distaste. The "lefty witch hunt" loses even more cogency when you notice that 33 of the Liberals were in favour of the Commission and 11 British Conservatives out of 28 were against it. This was the real stuff, and it's almost a pity that Barroso chose to give in rather than force a vote.
Secondly, there are very good reasons for the EU to remain secular. The settlement between the member states and the organisation is based on a division of powers. One of the areas the EU does not touch on is the content of national constitutions. If we are going to have secular France, devout Poland, a UK whose Queen is head of a Protestant state religion, and perhaps Turkey, a secular state with a Muslim population, in the same Union, we have to seek the minimum on which agreement can be reached. The minimum, in this case, is also the best answer - keep religion out of the EU institutions entirely. If the central institutions take a turn towards militant secularity, this will be unacceptable to many of the member states. The same goes in the opposite direction. Only at the zero point is this issue stable.