..the possibility of malware infection of voters' computers.
You need to either be ok with that (i.e. botnet owners should have more votes than normal people, because the whole reason that people give their computers over to botnets, is that they want to personally have less power) or else you need to give up on the idea of online voting.
And since nobody sane is going to be ok with that (I think people will disagree with my above parenthesized assertion), then: give up on the idea online voting. By the time you "solve" the compromised-user-agent problem, you'll have lost 100% of the reason for online voting, as we see with the amusing idea of making people use multiple computers which are hopefully on competing botnets and therefore unable to reach enough consensus to vote the same way.
Just keep having people go to polling locations. Really, it's ok to do that.