Just go to the iTerms2 preferences -> Profiles -> Keys -> set the Left/Right Option key to Esc+.
First I should say that Super brings up the big overlay grid, that is called the Dash. Tappipng Alt brings up the HUD, a smaller text field in the top left. It's a 'type-a-little' interface to all the commands in system and application menus. We can get a link for more info, if needed.
So you can shut off the Super key, with the low-level tool Compiz Config Settings Manager. The package name is compizconfig-settings-manager, if it's not installed yet.