Are you sure it's 2 YEARS?? I've heard of a "slow kill" method that some rescues use, it involves a 2 WEEK regimen of Doxycycline (an antibiotic), then after that you give the dog 2 heartworm pills a month for about 6 months. Two years of antibiotics sounds a bit extreme and not sure if I would be willing to do that to my dog.
I have recently been researching natural/holistic heartworm prevention and think I might go this route with my own dogs. Still not found enough information though to be sure of which supplement or treatment method is safest and most effective, so I am holding off until I know more about it.
I have read on another dog forum that this all-natural product has been successful in treating existing HW infestations. I don't know anything about it but you might consider looking into it.
HWF (Formerly HeartWorm Free) - Products
Also wanted to add, I recall reading on a holistic vet's website, he has kept his doggy clients HW-free using Heartworm nosodes, which is basically like a "holistic vaccine" against heartworms. Try looking up holistic veterinarians near you.
Good luck with your pup!