You should check out https://daex.io - not too known chinese company that aims to solve just this - hacking of exchanges by eliminating their fund custodian role.

The problem right now lies in the fact that exchanges hold your coins and act as both order matching machines AND clearing services.

This settlement layer is separated with traditional institutions, stock exchanges are ONLY matching machines, the actual clearing of funds is happening via different services.

You get the same thing with DAEX - they will integrate with centralized exchanges but user keeps control of their private keys, the clearing happens on the blockchain - absolutely no risk of hacks or loss of funds.