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.