Question:

 I would like to know if it is possible to use the qualification function (function of the GPIO) when the input is dedicated to a peripheral (in my case trip zone)?

Answer:

The qualification circuitry is active regardless of the setting of the GPIO mux.  So, yes, you can use the qualification for the peripheral function (trip zone).

Also refer to: http://processors.wiki.ti.com/index.php/Category:General_Purpose_IO_for_C2000