Online Schema migration in MySQL : When to start?
I think that Percona's pt-online-schema-change might be a better solution for you as it can do an ALTER with very little downtime. It does, however, require adding a TRIGGER to the table. 

Runnig DDL on your table will lead you into rebuilding your table, mysql is a row based engine so you will suffer the index rebuild this can be quite expensive depending on your engine, table complexity is factor as well.