There's a few different ways to verify, a few of them involving stopping replication, like you pointed out. These can also sometimes be quite expensive, so depending on the type of verification required, the verification method can be tuned.

We also implemented table checksums inside of mysqldump, allowing us to dump out the restored data and compare checksums as well, if required. https://github.com/facebook/mysql-5.6/commit/54acbbf915935a0...