In a word, no.
They’re certainly enough for Pullman to have been burned at the stake a few centuries back, but once you dig past the surface they’re not actually anti-religious. If you want to stay on the surface, like many aggressively atheistic teens (we all were one or knew one) that’s fine, great for you.
But the books really are more against religious delusion than against religion. Extreme religiosity is the villain, and false religions. God is an old man who disintegrates on the wind–but he’s not really God, even in the books, is he? He’s just a puppet, or a claimant to a title that was allowed to pass into his hand.
I’ll say this: the books are definitely anti-original sin. The victory of the books is to replay original sin, to reawaken knowledge. But, of course, if God knows all then he would have known that Adam and Eve would stray. So it must have been in the plan. And, after all, it is an Angel who protects Will and Lyra long enough for them to become Adam and Eve.