The simple answer is: Yes, rainwater is harmless to health.
Rainwater is evaporated water, comparable to absolutely pure, distilled water. As it passes through the air and runs off over the collecting surfaces, the absorption of impurities is rather low. Extensive scientific studies have been carried out on this, such as those by Holländer, R. et al. (1996).
The authors found that [...] when [rainwater] is used as service water in the household (toilet flushing, laundry, garden irrigation), rainwater collected in cisterns does not pose a " hygienic risk". [1]
A total of 1600 water samples from 102 different cisterns were used for the representative study.
[1] Holländer, R. et al..: Microbiological-hygienic aspects of the use of rainwater as service water for toilet flushing, garden irrigation and laundry. Das Gesundheitswesen, issue 5/96, Georg Thieme Verlag, Stuttgart, New York.
Cisterns & Complete Sets