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

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?