There will be no central website that is necessary for BCE to work - there will be lots of websites to grant convenient access to the trading functions. If you favourite website is unavailable, you can use the standard client (wallet) as well; the websites do nothing else but provide a user interface that uses the wallet via RPC in the background.
Creating such websites could be assisted by BCE with “kits” that allow easy deployment.
And if hackers want to spam the blockchain with transactions, they need to pay for it. Let them come!
My take is that BCE is quite safe due to its decentralize nature - there are no single points that can be attacked!