Safe online dumping of an InnoDB database in the presence of DDL changes
You could isolate the dump by placing it on a replication slave and stopping the replication before the dump.

As table modification isn't transactional, changing the isolation level won't help.

If you keep the binary logs (and use --master-data) with mysqldump, you could revert to the previous backup and replay the binary logs. This would be immune to the impacts to an single inconsistent dump.