I think it's possible to create a more secure exchange by using Nxt AE and Nxt messaging system. If the communication between the server and users is done via Nxt blockchain with no frontend, the server will be immune from hackers as they won't even know the location/IP address of the server.
It would work like this:
(1) A user would request to generate depositing BTC address in the Nxt client by sending a message to asset issuer.
(2) A remote server (or servers) (whose location and IP would be unknown so can't be hacked) would see the request on the blockchain and generates an address for the user and send it back via blockchain (normal Nxt messaging transaction). The client on user side will only have to check if the message received came from asset issuer address.
(3) The user can then deposit BTC to that address, and the secret server would update the users "bitcoin balance" by sending bitcoin asset to the user.
(4) Those BTC can be traded with other users via asset exchange
(5) Since no one would know the IP address of the secret servers, the servers would be pretty safe from hackers. No weak frontend. No usernames, no passwords, no 2 factor authentication no https.
(6) BTC could be withdrawn by simply sending the asset back to asset issuer with withdrawal address in the comment (the client will check to make sure the withdrawal address has valid format).
This would work for ALL ALTcoins (not just BTC) and it would be simple to implement by just modifying the default JavaScript UI of Nxt, which is open source already.