As best as I can remember, very few conclusions were ever reached, although there was certainly a Christian slant to the debates -- on e.g. abortion and euthanasia, etc. Nevertheless it was a minor element and the aim was to encourage people to think about this and to consider contrary views, rather than to reject such views out of hand. One debate I remember, is one where the house believed that the world "would be a better place without religion". The ayes had it! So, in my opinion, while implicitly Christianity was taken to be factual, it was rarely made explicit, and when it came down to it frequently the atheist position won out.
So in conclusion, I think you are wrong to say that this particular faith school was a centre of indoctrination, or some such. On the other hand, I doubt that this is the case in most faith schools, so perhaps I was just lucky.
In the long run faith schools ought to be phased out but only as a matter of course rather than as an imposed view. Many new faith schools are part of the new free school programme for example, so clearly the parents must want them. What with religious freedoms being protected by the Human Rights Act, it's hard to so that we can shut all such schools down overnight without an uproar and a legal challenge that atheists would lose. Better to try and drive people away from the extremist stances of their faith and hope that in the long run this will lead to them growing away from their faith. This is already happening, slowly, in the Western world as a whole.