I’m trying to fix the simple issue of WordPress not allowing “tel:” links in menu items. I found this patch which fixes the problem, but I have to edit the core file which is not ideal. Any WP masters out there who know of a way to add a protocol to this array via a theme’s functions.php?
Applying a WordPress patch through a theme’s functions.php
Take a look at Hotfix plugin – http://wordpress.org/extend/plugins/hotfix/
It basically does this by locating function and overriding it. In your case, try overriding “wp_allowed_protocols”. (looking at 3.3 code)