What if the "spirits" people worshipped were tied to one of the greater gods. In other words, worship the spirit of this well, spring, creek, river or whatever, but know that it is only a minor aspect of the great goddess?
Or the spirit of your dead ancestor is actually a fragment of the god or goddess? It can intercede directly with her because you are its decendant, but otherwise it is not going to help you.
This keeps the focus clearly on the greater gods, but gives a slight softening and makes them approachable. And anyone can worship their ancestors. Look at some of the current Japanese and Chinese belief systems. They're certainly not all followed only by rural peasants!