I like letting it run, but I haven't (yet) done the research to compare how much work the villagers do that way vs. quitting the game for a while. (Though I will quit if they just finished harvesting the field and it is XX minutes until there are new crops... I don't want them getting too distracted/tempted by watering the crops.

I also found that running the game on 1/2 speed will earn points faster per villager "year" than on normal or 2x speed. But you need to have the patience for the nursing/harvesting cycles in order to take advantage of that.