The hand-filled ballot seems safer, few people are going to check every single race to make sure the printed ballot matches -- my ballot had about 2 dozen races to vote in (it included a bunch of judges, school board positions, etc), that's a lot of double checking. Make the person fill it out by hand first, then read it by computer.
WA conducts vote by mail like this, and it works fairly well; we’ve had scantron technology for decades at this point.