Good heavens above. What about all the dogs in the wild? How many dogs do you know that love to eat a birds, rabbits or some other animal raw?
In my opinion your new pup is more likely to have far more problems from eating the Eukanuba (or any commercial dry food) than it is from eating raw meat.
My pups are raised on a raw diet and never eat cooked meat. They have raw chicken necks, wings, frames etc as well as raw beef, lamb and pork either minced or in chunks. Although for the young pups - up to about 6 months I do tend to use human grade food.
I have fed raw meat for over 30 years and never yet had a dog with an infection from the bacteria. Really these Vets have no idea other than what the dog food companies feed them, which is to brainwash them into thinking they have the best food and to convince "us" to feed the food the pet food companies want us to buy!
As far as I am concerned - and this is my opinion and it is not important to me how other people feed their dogs - feeding most commercial food - dry, tinned etc. is akin to feeding your children on McDonnalds all the time.
Find another vet and enjoy your baby. As for the heart murmer, as long as it is not a major one there is a very good chance that it will not cause any problems at all. This could also be a reaction to the vaccination.