Does turning off foreign key constraints prior to dropping the table help?
set foreign_key_checks=0;
drop table <table>;
set foreign_key_checks=1;
There is a bug report which details something similar, but I'm not clear if it is the same issue:
http://bugs.mysql.com/bug.php?id=5784
If not, you could try mysqlcheck:
mysqlcheck -u root -p <dbname> --auto-repair --check --optimize --databases
You'll have to check the docs for the most appropriate options for your database. Be sure to note the comments in the first paragraph of the docs about the locks that are placed on tables while this command is running.