Chinese and Ayurvedic does not have a lot to offer in terms of protozoa infections unless they are the lower level ones such as giardia. Chinese medicine calls these damp conditions and they state that these are quite difficult to get rid of. I tried numerous acupuncture sessions with no success, also have done numerous chinese formulas. I do self treatment on certain acupoints with a red laser pen and get some help but not enough to kill them.
It is interesting that the chinese will say that these infections 'invade the shen' which in english terms means 'patient goes crazy' :)