Is this yin, yang somehow measurable? If not then there is a fundamental problem.

Also Western medicine is very well aware of side effects, it's actually one of the fundamental concepts. For example it knows that taking Paracetamol is good against pain, but increases risk to the liver, especially when taken with alcohol. It's also very well aware of causes of fever and doesn't recommend lowering it for the sake of it, only from certain dangerous level. It also knows that taking antibiotics affects gut bacteria, so it's often recommended to take also probiotics. It knows that some medicine could affect women differently, especially when they are pregnant or are breast feeding. The list goes on, it's never black and white.