There's nothing at all wrong with using science to prove God. What's wrong is using bad science to do it.
If God went through all the trouble of creating science, I'd expect he'd insist on people engaging in a proper methodology when using it to demonstrate his existence. Anything else would just be rude and insulting to the man and he tends to burn folks in Hell for that sort of thing.
Science is a man-made process used to investigate the universe.... God just created the universe, is all. So, He created science like he created the internet.