A more important question to ask is: "Why IE11 is popping up that alert?".
Are you leaving a secure page for an insecure one? I.e. make sure to call the secure booking API, or let the browser choose, by not explicitly specifying the protocol:
var url = '//api.booking_site.url/api_endpoint';
This will call either the secure or insecure version of the url depending if you're currently browsing a secure or insecure site.
If you just want to get rid of the pop-up, assuming the pop-up you mention is an alert box, you can overwrite alert
:
window.alert = function() { return true; }