I'll start by mentioning my own question posted on stack-overflow about a year ago, and it's somewhat of the same question: How can I set client configuration for MySQL Workbench without an installed server?
As already mentioned in an answer here, as of MySQL WB 6 you can set the "leave autocommit mode enabled by default" preference in Preferences > SQL Queries > General.
For earlier versions it might be possible to configure the "my.ini" file.
Why only "possibly"? Because it worked for me before (WB 5?), but doesn't work now on WB 6.3.
First, we need to find out where does WB is looking for the file. There are several questions on that subject, so you might have to fiddle with it a little (frankly, it's a messy issue).
The best way, if available, is to go to the Server menu and then press "Options File". It will either tell you that the file doesn't exist (and will tell you the path it's looking for), or it will open the configuration and will specify the path at the bottom.
Now, we need to add the following line into the "my.ini" file, under the
[client] section (add it as well if it doesn't exist):