The crystal frequency sets the clock speed of the whole circuit. Clock speed is directly related to pitch. Think about it like a record. If you increase the speed of the record, the pitch goes up. 

Fading between two crystals will not fade the pitch smoothly. At best it will just switch between the two without any transition. More likely the circuit will stop functioning as you try to fade between crystals and will only work at either extreme of the potentiometer adjustment (all the way up or down). Fading between crystals will only modify the amplitude of those two signals. One will decrease amplitude while the other increases. In the middle you will have a mix of both signals at mid amplitude.  
In order to change the pitch of the circuit you need to change the frequency of the clock not the amplitude. Changing amplitude will just make the circuit not "see" the clock and it will think there is no clock/ it will not work. 
Unfortunately the frequency of a crystal is inherent to its crystalline structure and can not be modified. It's possible to replace the crystal with a high frequency oscillator which CAN be adjusted but that requires the creation and installation of a new circuit.