As far as I know, interception of civilian aircraft is done to assess a situation where the safe status of a flight is uncertain.

A Vueling A320 [got intercepted][1] some time ago when the Dutch ATC [weren't able to communicate][2] with the pilot. Intercepting the aircraft and watching the situation inside the cockpit and/or the cabin can help to assess whether there is a serious situation developing (and further actions can be taken) or just an ordinary human error/technical fault. I think it's just a matter of gaining some time if a hijacking occurs.


  [1]: http://www.youtube.com/watch?v=zmvh2wP1BHs
  [2]: http://avherald.com/h?article=4550b86c