App Engine expects your web apps to return almost immediately (in a matter of few ms). For anything that takes longer, you need to use task queues in App Engine. Or maybe try AppEngine Managed VM's?
If you run multiple modules at once (some serving the frontend, some for longer tasks w/task queues), you can have the best of both worlds and use different scaling options for each.
(I also work at Google, but also not on App Engine)
