So how do you stop someone removing that USB drive from the port from inside the voting booth, inserting an infected USB drive, contaminating the machine, and replacing the official USB drive?
Instead of trying to make the computer be smart and tabulate the votes, use it in the simplest way possible. Let it do nothing more than provide an easy to use touch screen interface and print out the completed ballot with uniform markings (no more “hanging chad” questions) both in human readable and machine readable (QR code, perhaps) forms. Most voters could then confirm that the ballot reflects their intended vote via a smartphone app.
Have a vote tabulator / ballot box into which voters insert their ballots (face down) in a public, visible location through the whole time the polls are open. Let anyone who wants to observe that it is not tampered with through the day do so (as long as they’re not trying to intimidate voters.) That ballot box will count the machine readable votes. Fall back on the human readable votes, uniformly printed on the paper ballots, as a spot check on the accuracy of the ballot box and in the event of a recount.
The printers can be used in government officials’ offices while they’re not in use on election day. If you went to a big box electronics store like Best Buy, you could probably pick up Android tablets for $100-$200 dollars that would work perfectly fine as the touchscreen interfaces. Alternately you could get all-in-one machines that would be usable both for day-to-day government work and voting duties for a couple hundred dollars.
The most expensive part of that system would probably be the ballot box, and if you want to rely just on the human readable vote and manual tabulation all you really need is a lockable box with a slot big enough to slide the ballot into. Staples has a drop box for about $30 that would probably do the trick. It’s only 3 inches wide, putting a limit on the number of ballots it can accept, but they’re $30 a piece – get a couple of them, it shouldn’t break the bank.