Pullman does no worse than any other modern writer by making controversial statements - they all do it over something or other. Tolkien himself wasn't averse to stirring things up a bit, he makes a sarcy comment in the introduction to Rings about what he thinks of his detractors (nice one, Tolkien)
And you can find statements elsewhere from Pullman where he gives Tolkien more praise; however nastiness sells copies of Sunday papers to the Brioche munchers of Islington, so that gets picked up on.
Personally, I didn't 'get' the Christian references in Lewis either and I picked those books up when still (just) a Christian. I just thought they were rubbish in comparison to Tolkien, who had I had just finished reading. Despite what the higher message of Lewis might be about Susan I still think them not great choices to give to a young girl to read unless she is possessed of strong self-esteem. Kids do look at 'surfaces' and seeing a girl condemned for something as normal as wearing lipstick is just not fair. Not saying young lasses should not read these books, just that there are now loads of far more appropriate books with better heroines.
I just wish I could find again the page on Gaiman's blog where he talks about his disappointment in finding out what Lewis said Narnia was 'about' - he says as a young lad he felt cheated. I'll keep looking for it...
I suppose my main beef with Narnia was just that it was so....
twee.