Sony probably wanted to really make sure that their system was secure (well... as best as they could make it).
Alternatively, they may have decided to rebuild portions of it to try and improve the security.
Still, it seems like an inordinate amount of time. Like, they weren't just caught with their pants down, they had no pants at all and needed to make new ones from scratch.
So many other companies/organizations that get hacked (banks, government, etc) don't have any noticeable interruption of services, they just get things fixed asap and then try to figure out what happened. I think Sony should have just put up online services but pulled the PSN-store until everyone is notified about the credit card info being stolen and they can secure the data better.