With
FileMenu Tools you can add some custom sub menu items.
On the tab "Commands of other applications" you should be able to locate and disable Microsoft Security Essentials and Malwarebytes context menu entries.
You can also use
ShellMenuView to locate Microsoft Security Essentials and Malwarebytes context menu entries (back them up!!! before deleting). But unlike first program, ShellMenuView works only one way - you can disable old, but can not create new entries.