I suppose there's nothing Apple can do about this in all honesty, not sure if they would. But after Google Voice not being allowed in the app store for so long it is something that apple may not like.
As I recall, their issue with the GV app was that it "duplicated features" like the phonebook and dialer. Whether you believe that was their real reason or not, the Sprint integration doesn't duplicate anything - everything can be done using the native phone functions.