Ok, based on the comments, I decided to just prevent activation and send an admin notice instead.
add_action( 'admin_notices', 'lsmi_admin_notice' );
add_action( 'network_admin_notices', 'lsmi_admin_notice' );
function lsmi_admin_notice() {
if( class_exists ( 'Location_Specific_Menu_Items_By_City' ) ){
global $pagenow;
if( $pagenow == 'plugins.php' ){
deactivate_plugins ( 'lsmi-by-country/LSMI_Country.php' );
if ( current_user_can( 'install_plugins' ) ) {
echo '<div id="error" class="error notice is-dismissible"><p>Error. Please deactivate LSMI by City first and try again.</div>';
}
}
}
}