That's like saying "Everyone whose been shot died because of the person who invented guns". The journals were instruments of research and occasional use as a diary. Stanford is a scientist. He made the tools and he studied Gravity Falls. In turn, he created weapons and defenses. I hardly think Stanford thought to himself while writing the journals: "I sure hope some people come across these and use them for mass destruction!" He was most likely thinking along the lines of being an esteemed scientist and having his name known everywhere by everyone.
He created those journals for his own sake. Because of who he trusted, he ruined his own life and ended up dragging Stanley with him. He hid the journals to keep the world safe and instead two kids stumbled across them. Gideon and Dipper both found the journals. While Gideon was using it for mass destruction, Dipper was using it as intended: an instrument of research. In the process, Gideon tore apart his family and Dipper started going down the same road to paranoid insanity as Stanford did.
If anything is to be gleaned from this, it's that knowledge is, in it's very definition, power, but is not moral nor immoral. It's the user that makes it so.