You want to create your own baking theme so that you can then edit the template to delete the file.
It really is that simple, http://book.cakephp.org/2.0/en/console-and-shells/code-generation-with-bake.html#modify-default-html-produced-by-baked-templates
Just copy the files from inside lib/Cake/Console/Templates/default/views to your project under app/Console/Templates/[themename]/views , and then you can edit the presentation templates.
The same applies to all other files, such as controllers and models. Then, when you bake your project, you will be asked what topic you want to use, and you can choose your own.
Here is an example from one of my projects.

The only thing to note is that the names of your themes must be unique!
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