I wouldn't tale the controversy too seriously -- that mainly arise from the religious right in the US, as evidenced by the fact that the controversy didn't start until years after the books had been popular hits in the UK. Over here I think the main complaint was that the message became heavy-handed towards the end, rather than the themes themselves being particulary groundbreaking. Pullman's clarified in interviews that what he was really attacking was fundamentalism, rather than religion as a whole.

I havent seen the TV series but it sounds like they're doing a better job than the film...