What is a natural alternative to having a child vaccinated?

There Isn't One. There are no complementary or alternative medicines to vaccinate a child. There are only two ways a child becomes immune to a particular disease: a) having the disease and recovering from it, or b) being vaccinated.
Pray You are Lucky. There are no proven natural, organic or homeopathic alternatives to immunizations. Thus you have to hope your child does not come down with life-threatening vaccine preventable diseases and if so, that medication is available to maybe save their life. Despite medicine's best efforts, prior to the hib vaccine 2-3000 children died yearly from this disease in 2010 it was 2.This was due to the vaccine.
Agree. Correct. The alternative to vaccination is not to vaccinate. Some practitioners recommend homeopathic nosodes as an alternative to vaccines. They work great if there is an epidemic to help prevent illness. Homeopathic vaccines do not stimulate antibody response. Maintaining a healthy immune system is your best bet. Chinese medicine / homeopathy are worth researching.
Build up immunity. You can build up immunity in children by giving them iodine supplements. When there is any ache or feeling of flu like symptoms immediately use propolis with honey and have them take this orally kills germs immediately. Also use nac and bromelain during flu season gives extra cell energy and helps body fight the flu germs.