Whilst I agree with the ruling, I find it deeply sad that it came to law at all. Secularism is all about religious freedom; we shouldn't be in the business of 'banning' things.
The problem comes because some people think, just because they are generally free to do a thing, they should be allowed to do it whenever and wherever they like, regardless of the implications for other people. This applies to many issues of freedom, not just this case. Commonly, this is known as bad manners. If people have good manners and are considerate of other people, you don't need to make rules to govern their behaviour.
We shouldn't have to prevent councils from holding prayers in their meetings, for the same reason we shouldn't have to prevent them from playing football. "Why shouldn't I play football in council meetings? We've always played football - it's a tradition going back hundreds of years. This is a football playing country. What do you mean it excludes people who don't want to play? How dare you challenge my right to play football whenever I want? You should respect and tolerate my football playing."
Obviously Christian councillors should hold their prayers, and their football matches, outside of the meetings. There should be nothing more to say on the matter, but if Christian councillors are going to be selfish and continue playing football during the meetings, we're going to have to make a rule saying they can't do that. It is just a shame we could not rely on common sense and good manners to get the same result.