How do I modify the new 4.6 CiviMail form?
I ended up adding a small bit of javascript that waits for Angular to build the form, then it disables the checkboxes. Don't know if it's the right way, but it works.

CRM.$(function($) {

function disable_tracking() {
    var i = $('#tab-tracking').length;

    if (i &gt; 0) {
        $('input[name="url_tracking"]').attr('disabled', true);
        $('input[name="open_tracking"]').attr('disabled', true);
    }
    else setTimeout(disable_tracking, 250);
}

if ( (typeof(CRM.crmMailing) == 'object') &amp;&amp; (CRM.vars.sendgrid.track_optional == '0') )
    disable_tracking();


})