Killing anyone in a faction, not just shopkeepers, will make that faction hate you.
There are 4 different `kill 100 enemies' missions, one for each of the 4 factions. Easiest ones to get this achievement on is either the village or town, since the battles take place in areas with a lot of open areas. Fujimori or the other faction gives you the quest in a really lousy area with lots of trees and stuff blocking your way.
There's really no other way to get this achievement. Most of the other huge battle events cut off at about 30-50 kills.