step down 9V AC to 6V AC without transformer
Work a little harder at finding a transformer with two secondary windings. This should not increase the size of the transformer much. 

Alternatively use the one that you have with the 9VAC output. Rectify the 9VAC to DC and then use a voltage regulator to step that down to the needed 5VDC. This can be done with a cheap linear regulator such as a 7805 if the current load is very low. It the load current has any size to it at all the temperature created by power drop in the regulator can get prohibitive and so a better recommendation to convert the rectified voltage to 5V would be with a switching regulator. Once you have the regulated 5V then use a low drop out (LDO) linear regulator to further drop the 5V to 3.3V for the low current crystal oscillator load.