Encrypting a Database row-by-row
You're paying the extra price of network IO and there's not a whole lot you can do if you need to remove the encryption (really the key storage/management) from the database. If your MySQL instance is on a Unix host, you can try connecting with a Unix socket file instead of TCP/IP. Just host the app on the same machine during the encryption process, finish the DB then move the app back to wherever it should be. 

If your MySQL DB is running on Windows then you're out of luck. You could still put the app on the same machine or isolate them from the rest of the network so you minimize impact from network congestion or switch latency but those are likely to yield limited improvement unless your network was really, really busy or if you were using some old 100Mbps switch.