IMHO the # of true conscientious objectors in this country is a fraction of the # of people who just didn't quite get around to it. Especially in low socio-economic areas. Providing a strong financial incentive will increase vacc rates significantly in those communities and is likely to save the public health system a bucket load of cash in not having to treat quite nasty complications that arise in otherwise (statistically) preventable disease.
But that already exists. For those who don't get around to getting vaccines, they miss out on the bonus. My understanding is that the changes only affect current conscientious objectors - at the moment with a CO form they are considered up to date for centrelink reasons, with the changes they will no longer be considered up to date.