This multiple menu problem is fixed in mysql workbench version 6.3.3. I installed the new version found here:
I installed the following version Ubuntu Linux 14.10 (x86, 64-bit), DEB.
NOTE: Am am running Ubuntu 15.04. However, I installed the 14.10 version and it works just fine.
If you look closely, the menu is not actually doubled. It is actually two separate menus. The first menu is specific to the MySQL Connections home page. The second menu is specific to your open database connection. For example, if you open mysql-workbench, at first you'll only see one menu. Then, if you open a database connection and display an SQL worksheet, the second menu is displayed.
I would probably classify this as a bug because of the redundancy of the two separate menus. However, if you'd like to change the menus, you certainly do so by editing the XML for them here:
One way to do this is to run:
sudo nano /usr/share/mysql-workbench/data/main_menu.xml