When we create big mission arcs, we design them to be a fun, engaging, and most importantly, a linear experience. We want players to get a sense of story and to do something interesting. We also want to reward players who accomplish the goals for those missions. This changes when people farm missions, though. They're participating in a kind of experience that's not fun and not really what we had in mind when we put those missions in place.
Playing a mission over and over isn't really the problem by itself, even though it isn't what we originally intended. Even gaining a lot of money per hour by playing it over and over isn't the problem.