Dumbledore had to replace zir furniture after the fire. The Pensieve survived, though. (It's made of stone, and probably enchanted to be harder to break as well.)

Granger could have taken the Floo Network instead of using such a showy method of travel, but many people can access the Floo Network Authority records. Granger doesn't want any of zir enemies to be able to track zir location.

In the books, there are some sort of unspecified defenses that make it harder to fly towards Hogwarts by broomstick, in addition to the Anti-Apparition Charm and Anti-Disapparition Jinx that cover the castle. That might prevent Granger from using zir flight magic to enter the castle airspace. However, unless there's a hard barrier that blocks physical objects, there's nothing to stop Granger from falling to the interior of the shield and then flying the rest of the way as normal.