You can certainly play Village Sim in that manner, but (as you've already noted) your progress will be much slower than it would be if you allowed the villagers to work while the game is not running. Even though the villagers seem to goof off a lot when you're not controlling their every move, they are actually very productive. I've found that once a villager is trained in a skill, and I set that skill as their preferred skill, they will stick to the job well enough to produce results. Different villagers will have different levels of industriousness, but I've found that, overall, they will get the job done if I leave them alone. I still sometimes micromanage the little peeps when I'm actually running the game, but I don't usually pause the game when I'm away from it.

The only real problem that I've discovered with leaving the game paused for long periods is the one I described with the farm. Under normal circumstances, the farm (which has a finite supply of food with each crop cycle) will be depleted periodically. If you have few villagers and only 1 or 2 farmers, they may not be able to gather enough food to harvest all of the crops before the next crop has grown. In that situation, you will see crops on the farm continually. If you have a lot of villagers and many farmers, it may take very little time to harvest all of the crops, at which point the farm will be empty until new crops grow.

The best way to tell if the food supply is adequate and reliable is to monitor the food that's available in the bin and check the "Food harvested" statistic on the stats page (which will tell you how much total food has been gathered).