in the case of drugs we are using the scientific method. The drug is a real substance, and it's effects can be tested.

In the case of faith healing, etc, the 'god' is a non-real entity, in other words, it cant be seen, felt, tested, or analyzed. There is no means to ensure that poeple are really praying to a god, or that the god will pay attention. No matter how consistently poeple may be healed, science has to look for natural explanations. Gods are not an option.

So even if 1000/1000 poeple prayed to god/gods and were healed, science must regard this as either a statistical anomaly, or a real correlation relating to something naturalistic, such as genetics, physiology, etc. In niether case can the prayer be considered causal.