The music of Rush has never been about sex, drugs and rock & roll. Their music has always been on a higher level with positive messages. I don't see these current lyrics, or those from the past being anti-God. However, I do see them as being anti-organized religion. There is a difference.
I believe that a lot of the songs with similar lyrics, past and present, are meant as a slam against the intolerance and ignorance that some fundamentalistic religious beliefs foster.
A common theme I see that runs through many of their songs is a strong belief in humanity and that if we work together, instead of being divisive by religious conviction, we can fix a lot of what we ourselves have somehow screwed up.
In other words, don't blame God for everything that goes wrong, and don't just sit on your butts waiting for him to fix things either. If we work together instead of being divided, we have a good shot at accomplishing something.
These are messages of hope and love for humanity. And what was Jesus's most important commandment? So, how can you get more spiritual than that.