Is it better to let diarrhea run its course or to take pepto bismol ?

Pepto Bismol would never be harmful or delay clearing of the diarrhea, no matter the cause. If it's serious diarrhea, PB won't work, but it's fine to give it a try.

It really depends on the cause of the diarrhea. If it is a periodic, episodic cause such as viral gastroenteritis, the diarrhea usually will resolve spontaneously. If the diarrhea is due to a chronic process, the underlying issue needs to be solved. see your primary care doctor or your gastroenterologist for more evaluation and advice. Good luck.