You can use remove_meta_box() to accomplish that.

To use remove_meta_box() you will need 3 pieces of information:

1. the id of the meta box you want to remove
2. the screen (or screens) you want it removed from
3. the context it was added in (e.g., ‘side’, ‘normal’, etc)

To get these 3 pieces of info, search thru the source for the theme for add_meta_box() call(s) that are used to add the meta box.

And in case it’s not obvious, make sure you call remove_meta_box() in an action that is fired after whatever action the meta box was added in.

For example, if the theme looks like:

add_action ('after_theme_setup', 'add_theme_meta_boxes') ;

function
add_theme_meta_boxes ()
{
    add_meta_box ('ad-to-upgrade-to-pro', 'Upgrade to Pro', 'render_upgrade_ad', 'post', 'normal', 'high') ;

    return ;
}

The your plugin should contain the following:

// make sure you hook to an action that is fired *after* the meta box was added
add_action ('init', 'remove_theme_ad_meta_box') ;

function
remove_theme_ad_meta_box ()
{
    remove_meta_box ('ad-to-upgrade-to-pro', 'post', 'normal') ;

    return ;
}

Edit

To answer the question asked in comment: it is not possible to absolutely guarantee that no other theme/plugin adds meta boxes.

Besides, with an open system like WP, it is not a good idea to do what you are trying to do (IMHO). There are a whole host of “general purpose” plugins out in the wild that have legitimate reasons for adding meta boxes to your CPT’s post{,-new}.php screens.

For example, the WordPress SEO plugin adds a meta box to any post type that is “viewable” that allows adding SEO-related metadata to the public page for posts (note: mention of WordPress SEO is not meant as an endorsement, it’s just the 1st one that came to mind).