These variables are located immediately after defining a local copy of jQuery in the jQuery source.
// Map over jQuery in case of overwrite
_jQuery = window
Javascript doesn't have the means of providing the kind of protection you are looking for.
JQuery isn't "protecting" those variables. It's just copying the references $ and jquery into two other variables. The code you have read is equivalent to:
var obj1 = {}; /* create an empty object and reference it as obj1 */
var obj2 = obj1; /* made a second reference to that same object */
This code doesn't "protect" obj1. It's perfectly valid that your code later on changes the value of obj1:
obj1 = 'foo'; /* now obj1 references a string */
obj1 doesn't "magically retain its value"; after that line, it's just a string. But the object is still available in obj2.