Ok, done.
I'm really impressed with this series, and it ended just as I thought. My understanding is that it isn't against religion at all, but instead against the sects of religion that are old, out-dated, and continually attempt to assert dominance and control, to do bad things to other, to lie, yet try and claim them as done in the name of good.
Lyra and Will had to make a decision, and that decision was not good or evil, but a choice. They had to choose the lesser of all evils for the better of all humanity in all worlds. They could leave one opening without affecting spectres or by it killing adults. They could be selfish and leave one open between their worlds so they could see each other, or they had to say goodbye forever to each other, leaving only the one they created for the land of the dead, so those honest souls could move through death and become part of everything around us all. They become dark matter. Dust. The universe.
I found this quite a profound read. Very enlightening.
One could really relate this in muslim religion. There are millions of muslims globally who are devote in doing good, living their lives helping others, etc etc. Then you have those small in number who corrupt the understanding and meaning, and attempt to justify doing evil in the name of good.
There is a huge history for both Christianity and Islam, in small parties giving both religions bad names. The majority of all within them are good people, doing good within the world. But there are always selfish individuals within, selfish groups, who try to justify their evil under religious indifferent meaning.
A truly eye opening read and enjoyable read.