In reality, a lot of weapons from around the world (including Europe) had their origins as farming tools.
In Europe, there were many times (in many countries and regions) where they rounded up peasants to use as additional combatants in battles. It wasn't that uncommon to see commoners fighting alongside trained soldiers. In many cases, the commoners fought with whatever they had at hand, including various types of tools.
In the real world, although it's always a benefit for a combatant to be a trained fighter, that doesn't mean that (s)he will always win against a person who has little formal combat training. A lot depends on the circumstances of the combat, the people involved, and more.
Depending on the culture, some farmers may be quite skilled in folk combat methods. There are a lot of "folk" wrestling traditions spread throughout the world, along with some that focus on particular weapons (like knives and machetes) Some cultures place a high value on fighting as a means of gaining social stature, as well, so you may end up with a farmer (or other everyday person) who has a considerable amount of experience with combat. At various times, Sicily, Albania, and Ireland (just to list a few) have produced a lot of fierce, dangerous combatants with no "formal" training.
Pathfinder doesn't really support that within it's very limited class structure. In your example, he gets the weapon mechanics from being an Inquisitor, and the farming knowledge from being a farmer in the past. There's no reason you can't say that he's good at using a scythe because he was a farmer, as long as you have the feats and class features to back that up. The explanation doesn't have to match the mechanics precisely.