You can disable jetpack shortcode options but it will disable all jetpack shortcodes: In your dashboard, click jetpack in the sidebar, click deactivate on the Shortcode Embeds box.
Comment one line in the jetpack plugin. This has to be done every time you update jetpack: In your dashboard, click editor under plugin in the sidebar, on the top right corner select jetpack by wordpress.com in the dropdown menu, click select. Click on jetpack/modules/shortcodes.php in the list below, then click on jetpack/modules/shortcodes/soundcloud.php. In the editor find this line
add_shortcode( "soundcloud", "soundcloud_shortcode" );
and replace it with
//add_shortcode( "soundcloud", "soundcloud_shortcode" );.
The jetpack plugin basically bring many shortcodes with itself. It's great if you're only using jetpack and if you're happy with their basic shortcodes.
This fix can work for any of the shortcodes. you just need to select jetpack/modules/shortcodes/vimeo.php for vimeo, jetpack/modules/shortcodes/youtube.php for youtube, etc... and comment the line that add the shortcode.