Science is a method, not a topic
The mere fact that a person investigates alleged phenomena in a particular field (e.g., alternative medicine) does not make their work scientific, pseudo-scientific or anti-scientific. What matters is the approach and methodology they bring to the work. The fact that you presume that working with others who are interested in alternative medicine means that your advisor is involved in pseudo-science means that you are in a poor position (in terms of scientific maturity) to judge this issue.
Experienced academics with good track records of research typically do not require career advice from upstart PhD candidates, notwithstanding the pretentions of the latter to adjudicate for them what is and isn't real science. Your supervisor sounds experienced enough to make this judgment himself.