Multi-AZ RDS deployment is supposed to protect you from that though. That's why it's 2x the price. We should have failed over to a different AZ w/o EBS issues.
Maybe there was something bad with your replication server before the outage? It's hard to guess without knowing exactly what was happening at the time...
The whole point is to protect you from problems in one AZ by keeping a hot standby in another AZ. It doesn't matter whether it's due to EBS, power, etc. This is one of the primary reason to use RDS instead of running MySQL yourself on an instance.