I'm another who thought the last book was pretty awful, which was disappointing as I loved Northern Lights (the middle book was OK, but nothing like as good to my mind). I tried to listen to the radio version, which had Terence Stamp as Lord Asriel, which I thought was perfect casting until I heard him. I don't think I lasted 10 minutes. So I'll reserve judgement here until I actually see it.
As to the religious aspect, I can't see them toning it done, and not only because the bien pensants of the BBC are hardly renowned for their sensitivity to Christian beliefs. There's a vast difference between a film which is dependent in large measure on US sales, and the BBC's output, which would quite like US sales but isn't relying on them. The US is vastly more religious than the UK, both in numbers of believers and as a percentage of population, plus their more extreme and vociferous elements are greater in number and clout. There might be some complaints here about anti-Catholic bias, but nothing like there would be in the US. (And nothing like what would happen if the Ministry were based on, say, Hindu, Sikh or Islamic models which would really set the cat among the pigeons.)