First of all, hacking the electronic system is much much harder than hacking the paper process. In the case at hand the paper tallying process was the one hacked.
And second, electronic systems can create a paper trail, just make the electronic machine spit out a paper receipt. Then you have the best of both worlds, you can have instant electronic totals, and then do some random sampling recounts of the receipts to validate the result.
Scaling an attack against paper is incredibly difficult, and requires coordination in a level that is almost sure to trigger the law enforcement much before it can change some national-level numbers.
Scaling an attack against a computer system is almost the same as doing an attack against a computer system. Few attacks don't scale.
But yeah, if you just print the vote and push it into an urn (while the voter can read it), you'll get the best of both worlds.
And second, electronic systems can create a paper trail, just make the electronic machine spit out a paper receipt. Then you have the best of both worlds, you can have instant electronic totals, and then do some random sampling recounts of the receipts to validate the result.