Keeping the rabbits out is good (they carry coccidea and other nasties anyway).
Here is what Merck has to say about this:
Merck Veterinary Manual
They tend to go through the mouth, nose, and open wounds. Since there is obviously a problem in your area with these pesky critters, I wouldn't let the pups stay outside if they have any sores or wounds that could be penetrated easily. Also, even if it doesn't make total sense, there is promise with fipronil and (it looks like) imidacloprid. So Merial and Bayer may know more about this. If we had a problem like that here and Ellie went through that, I'd defnitely be choosing one of these products to try and prevent further problems. Apparently these things can even migrate to the brain. Not something I'd want to risk.