Sorry that you had this experience! I work in the medical profession. What your doctor says is true, it is endorsed by the American Academy of Pediatrics and by all vaccine companies as well. You really can give vaccines if a child is suffering from a minor illness.
However, having said all that, you did not deserve to receive a comment like you did. There is no such thing as an "overly concerned parent." And there is nothing wrong with being "eccentric," by the by, yet, in this context, this term was being used in a derogatory way.
I really hate to say this about my own profession...however, many physicians, pediatricians included, can and do have a tendency to look down on their patients as if they are stupid or don't know any better. It is related to the way some doctors are trained...sensitivity and compassion towards your patients is not something that is taught in most medical schools, and it also does not come intuitively to most. So it is quite common for doctors not to be able or willing to place themselves in their patients' shoes.
This comment is what I like to call a "tip of the iceberg" comment -- if this is what he is saying to your face, imagine what he may be saying to you behind your back. There are many wonderful, caring, and compassionate pediatricians out there, and it may be time for you to start looking for one. You want a doctor that is on your "team," so to speak -- not someone who will rudely antagonize you. There are ways to disagree with patients in a sensitive way, and a way to reach a compromise so that everyone is satisfied and patient care is not impacted.