MySql Master Master Setup w/ Rails Migration Schema

Problem: When you alter tables in the free version of MySql (not Enterprise) running on a master / slave or master / master replication, the replication will stop in it's tracks on any "ALTER TABLE" commands to one of the servers. Because rails uses this in migration.

Does anyone have a way of going about preventing this from happening, while the database is still live? My only suggestion is stopping the database replication. Running migration on both servers, then starting it again. But this is really risky I find.

Any other solutions?