I think the biggest issue is delivering the software.
In an absolute doomsday scenario (the Democratic party are literally North Korea, intend to overthrow democracy and install a one-party system), the machines could come pre-packed with the "right" software. A massive foreign power could probably build up the numbers of corrupt officials necessary to pull something like that off too. It's not like the US hasn't installed puppet governments around the world before.
Otherwise, it does introduce a challenge, but with a few surgical strikes you could probably swing a close election.
Some, for example, us a memory card. But that means you'd have to alter the memory card on each machine, which takes time and effort. Sure, you can prep them before hand but getting the manpower needed to stick enough of those altered cards in to ensure victory isn't easy.
And then you have the original votes which can be recounted by hand if there's a dispute.
I believe 5 states don't have a paper audit trail at all. Add to that numerous counties in the remaining states. Again, I doubt you could rig an election as clear as 1996 or 2008, but 2000, 2004 and 2012 are just about within the realm of slim possibility.