This circuit appears to apply 12V AC to the AVR input terminals in order to detect the zero crossing. You cannot directly apply 12V AC or about 17V peak to the AVR without damaging it. The circuit uses the limiting resistors RX and RY along with the internal clamp diodes within the AVR to limit the voltage. These internal clamp diodes were not designed to take alot of current. Therefore, I would start by limiting the peak current to less than 500uA.
17V/500uA = 34K ohms. Dividing this equally between RX and RY and choosing the closest 5% resistor means using 18K or greater resistors.
You could use only one resistor(34K or greater) and tie the transformer directly to GND. The original designer apparently used two resistors to limit the current is an unintended mis-connection is made.
For added protection, you could add external Schottky diodes in parallel with the internal clamp diodes, this will take some of the current load off the AVR.