When doing an ALTER TABLE statement in MySQL, the whole table is read-locked (allowing concurrent reads, but prohibiting concurrent writes) for the duration of the statement
If anyone is still reading this or happens to come here, this is the big benefit of using a NoSQL database system like mongodb. I had the same issue dealing with altering the table to either add columns for additional features or indexes on a large table with millions of rows and high writes. It would end up locking for a very long time so doing this on the LIVE database would frustrate our users. On small tables you can get away with it.
I hate the fact that we have to "design our tables to avoid altering them". I just don't think that works in today's website world. You can't predict how people will use your software that's why you rapidly change things based on user feedback. With mongodb, you can add "columns" at will with no downtime. You don't really even add them, you just insert data with new columns and it does it automatically.
Worth checking out: www.mongodb.com