I'm not sure Wells meant to say that science and technology were inherently dangerous or bad. Wells was a proponent of Darwin's theory of evolution. The conflict between science and religion is seen in the conflict between the curate and the narrator; interestingly, St. Paul's Cathedral is damaged, but the Crystal Palace, which was built to showcase technological advances from all over the world, was not touched.
You might say that a theme of The War of the Worlds is survival of the fittest. Despite death and destruction, humanity perseveres. The Martians just aren't fit to live on Earth.
However, Wells does show us that science and technology can be used for evil ends, as in the creation of war machines. The Martians themselves rarely appear; what the humans encounter is their walking machines. These machines devastate humanity, which we might be in danger of doing with the science of war.