pain came to konoha with the goal of finding the kyubi's host not to just rape everybody in sight like everybody is making it sound like.

yes he has cleverly disguised his search for naruto as an assault on the actual city itself but once he has found naruto or located his wherabouts his intelligence mission will be done and he will capture naruto and undoubtedly leave. (although i dont believe that pain will succeed in capturing naruto that is his plan though)

whether the destruction of konoha is a direct result of the way that pain chose to go about extracting info on naruto is a topic for discussion...