Spoiler Thread: Avengers Infinity War

Vision kills Thanos in the animated What if series, which is why I mentioned it. He slices him in half from head to groin, and Thanos had the rest of the stones. So, no, Thanos couldn't stop Vision if Vision was set on killing him. Remember, Thanos has to willfully use the stones, so, just make your way behind him without him seeing Vision and then blam, slice him up like deli meat. Problem solved.
Well, yeah, he did it in the animated series, but that's why it's What if... and not the prime time line. I dunno, I suppose you're right in theory tho.