So, after reading and thinking about the posts in the discussion and predictions thread I have decided to make a poll on Pain's attack and what happened to Konoha. Some people seem to think that Konoha was summoned somewhere else by Shima, Fukasaku and Naruto. Then of course there's the people who think it was partially destroyed like it appeared.
Personally, I think that Konoha was really hit by Pain's attack and not summoned elsewhere, or if it was it was still actually hit. The reason I say this is because of the following pages of the manga.
These pages show actual damage being done to Konoha so I believe it was actually hit, even if it was summoned elsewhere.
This is the last page in the chapter, notice the summon in the middle and a small crater in the middle of a large crater, this seems to be important to the people who think it was summoned somewhere else. Apparently the small crater is Shinratensei's blast radius and the large crater is where Konoha used to be.
I would also like to strengthen my argument with that last picture. It seems that you could still see the far regions of Konoha in the distance as well as the huge wall meaning it was not summoned elsewhere, unless only part of it was but I doubt that.
Finally, to support the "Other" option. The last picture could be a giant shield elevated above Konoha like the one Gaara made to defend Sunagakure. The large crater in this case would actually be the shield and the small crater would be Shinratensei's blast radius on the shield. Of course, the pictures of the damage being done to Konoha contradict this. I tried editing and making this an option too but you can't.