Let's keep it real.
Here is why: Stephen didn't believe in Heaven or an Afterlife. When you say RIP, you are implying that he could rest in agony which is....lets face it...him being in HELL. So if we really want to pay homage to this brilliant man just say "Remember Stephen Hawking" or "In loving memory". Something that doesn't directly contradict the person you're paying homage to. Hawking went farther than most would with his condition so, at the very least, we owe him this.