How to drop empty tables
The idea would probably be to look for the empty tables using INFORMATION_SCHEMA.TABLES

SELECT * 
FROM INFORMATION_SCHEMA.TABLES
WHERE TABLE_ROWS =  '0'
AND TABLE_SCHEMA = 'my_database_only'


Then you might be able to produce an SQL query with 

SELECT CONCAT('DROP TABLE ', GROUP_CONCAT(table_name), ';') AS query
FROM INFORMATION_SCHEMA.TABLES
WHERE TABLE_ROWS = '0'
AND TABLE_SCHEMA = 'my_database_only';


Quick and a bit dirty, but should actually work.