Q:

WordPress Multisite: Programmatically Activate / Deactivate a Plugin of a Specific Blog

Programmatically, I want to activate / deactivate a plugin of this specific blog/site in a WordPress Multisite. Any help will be gladly appreciated, thank you!

A:

Use a combination of switch_to_blog(), activate_plugins(), and deactivate_plugins().
You can put this in functions.php, but you'll want to remove it once it runs:
// hook to admin init
add_action('admin_init', 'wpse_swap_plugins');
function wpse_swap_plugins() {
    // set blog ID per your needs
    $blog_id = 3;
    // switch to the site where you want to activate/deactivate plugins
    switch_to_blog($blog_id);
    // activate: set your path, don't set redirect,
    // don't make this network wide, don't prevent activation hooks
    activate_plugins(array(
        '/full/path/to/plugin/you/want/to/activate.php'
    ), '', false, false);
    // deactivate: same arguments as activate
    deactivate_plugins(array(
        '/full/path/to/plugin/to/deactivate.php'
    ), '', false, false);
    // switch context back to original site
    restore_current_blog();
}

Credit to related answer: Deactivate plugin for a specific user group

