MySQL still brought down the server. Upgraded it to a newer version, and upgraded the tables.
MySQL and this webapp weren't getting along terribly well. Perhaps it's because we were using the old mysql gem rather than the mysql2 gem.
Everything is now using mysql2 and we're running against a newer MySQL so hopefully things will be better now. Watching things happen, and they seem to mostly be in the ruby process space, not in the mysqld process space, so I suppose that's a good thing. I'd rather have ruby doing the work, than mysql clogging itself up.