Ideally all exchanges should have halted trading at the same time. This would prevent bitcoin price changes during the frozen period and any issues such as yours from happening. Ideally an agreement between the large exchanges to implement a common circuit breaker somehow to halt trading for an agreed period of time when one of the exchanges prices change more than 10% in the space of a minute. If you look at the trade history Btc-e was first to have a flash crash. Bitfinex's flash crash happened 5 minutes later. Had there been a common circuit breaker then Btc-e would have triggered it and halt trading on all exchanges and thus prevent both the Btc-e and Bitfinex flash crashes from happening.

However I guess implementing this would be easier said than done and would require trust between the participating exchanges.