Fair, but a lot of people have emotional issues that make that difficult, and running can be a fun activity. Bonus: it helps someone learn just exactly how much that "100 calories" is worth - by converting into a measurement system that they already know (time to burn it off), it can help to prioritize eating goals in the future.
Exercise also has many other benefits beyond weight control though, such as heart health, overall musculature, blood chemistry, and more. thin != healthy.
But if we are getting this deep into it, running in particular isn't the best... it's quite hard on the knees I hear. An elliptical machine or something involving the body core like calisthenics would be easier on the body and more effective at the same time. Then again, running sure is fun... :-D