In your config file, add the following to set the default skin, changing the skin name below (larry, in my case) to whatever skin you are setting as default:
$config['skin'] = 'larry';
Then add 'skin' to the dont_override array. My dont_override is set as:
$config['dont_override'] = array(
'compose_save_localstorage',
'default_addressbook',
'default_charset',
'delete_always',
'drafts_mbox',
'dst_active',
'flag_for_deletion',
'force_7bit',
'junk_mbox',
'logout_expunge',
'message_extwin',
'mime_param_folding',
'reply_same_folder',
'sent_mbox',
'show_real_foldernames',
'skin',
'skip_deleted',
'timezone',
'trash_mbox'
);
Bear in mind that this will set the default skin, and remove the ability for users to change it going forward. But any user who has already set their skin to something different will still have that, as it will be stored in their preferences.