Disable and remove individual jetpack features.

functions.php

//To use place the function at the bottom of your functions.php file in the root of your wordpress installation directory.
function jherve_kill_monitor ( $modules ) {
	unset( $modules['monitor'] );
	return $modules;
}	
add_filter( 'jetpack_get_available_modules', 'jherve_kill_monitor' );

function jherve_kill_sso ( $modules ) {
	unset( $modules['sso'] );
	return $modules;
}	
add_filter( 'jetpack_get_available_modules', 'jherve_kill_sso' );

function jeherve_kill_notes ( $modules ) {
    	unset( $modules['notes'] );
    	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_notes' );

function jeherve_kill_comments ( $modules ) {
    	unset( $modules['comments'] );
    	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_comments' );

function jeherve_kill_carousel ( $modules ) {
    	unset( $modules['carousel'] );
    	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_carousel' );

function jeherve_kill_likes ( $modules ) {
    	unset( $modules['likes'] );
    	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_likes' );

function jeherve_kill_post_by_email ( $modules ) {
    	unset( $modules['post-by-email'] );
    	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_post_by_email' );

function jeherve_kill_omnisearch ( $modules ) {
    	unset( $modules['omnisearch'] );
    	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_omnisearch' );

function jeherve_kill_gravatar_hovercards ( $modules ) {
	unset( $modules['gravatar-hovercards'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_gravatar_hovercards' );

function jeherve_kill_contact_form ( $modules ) {
	unset( $modules['contact-form'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_contact_form' );

function jeherve_kill_widget_visibility ( $modules ) {
	unset( $modules['widget-visibility'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_widget_visibility' );

function jeherve_kill_photon ( $modules ) {
	unset( $modules['photon'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_photon' );

function jeherve_kill_videopress ( $modules ) {
	unset( $modules['videopress'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_videopress' );

function jeherve_kill_latex ( $modules ) {
	unset( $modules['latex'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_latex' );

function jeherve_kill_enhanced_distribution ( $modules ) {
	unset( $modules['enhanced-distribution'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_enhanced_distribution' );

function jeherve_kill_infinite_scroll ( $modules ) {
	unset( $modules['infinite-scroll'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_infinite_scroll' );

function jeherve_kill_subscriptions ( $modules ) {
	unset( $modules['subscriptions'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_subscriptions' );

function jeherve_kill_tiled_gallery ( $modules ) {
	unset( $modules['tiled-gallery'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_tiled_gallery' );

function jeherve_kill_vaultpress ( $modules ) {
	unset( $modules['vaultpress'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_vaultpress' );

function jeherve_kill_mobile_push ( $modules ) {
	unset( $modules['mobile-push'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_mobile_push');

function jeherve_kill_stats ( $modules ) {
	unset( $modules['stats'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_stats' );

function jeherve_kill_sharedaddy ( $modules ) {
	unset( $modules['sharedaddy'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_sharedaddy' );

function jeherve_kill_after_the_deadline ( $modules ) {
	unset( $modules['after-the-deadline'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_after_the_deadline' );

function jeherve_kill_publicize ( $modules ) {
	unset( $modules['publicize'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_publicize' );

function jeherve_kill_gplus_authorship ( $modules ) {
	unset( $modules['gplus-authorship'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_gplus_authorship' );

function jeherve_kill_shortcodes ( $modules ) {
	unset( $modules['shortcodes'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_shortcodes' );

function jeherve_kill_minileven ( $modules ) {
	unset( $modules['minileven'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_minileven' );

function jeherve_kill_custom_css ( $modules ) {
	unset( $modules['custom-css'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_custom_css' );

function jeherve_kill_widgets ( $modules ) {
	unset( $modules['widgets'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_widgets' );

function jeherve_kill_wpcc ( $modules ) {
	unset( $modules['wpcc'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_wpcc' );

function jeherve_kill_json_api ( $modules ) {
	unset( $modules['json-api'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_json_api' );

function jeherve_kill_shortlinks ( $modules ) {
	unset( $modules['shortlinks'] );
	return $modules;
}
add_filter( 'jetpack_get_available_modules', 'jeherve_kill_shortlinks' );

Added:
Single Sign On
Monitor

Any way to kill the Wordpress.com tools (manage) module ?