MySQL drop foreign key too slow?
Unless you are using InnoDB Plugin (and by default, in MySQL 5.0 and 5.1 you are not), removing an index require rebuilding the whole table.
If you can't upgrade MySQL, you should either look at online-schema-change (involving transfering all of the data to a new table without the index) or stop the site, minimize any I/O activity and wait the operation to complete.