Since you are interested only in frequency, and your system already handles the signal when it is at its lowest values, then the only problem is sawing off (clipping) the tops of the signal when it is above 3 V. This can be done with 1 resistor and 1 zener diode.
The resistor is in series between the sensor output and the uC input. The zener diode is in shunt across the uC input to GND. Connect the cathode to GND and the anode to the A/D input, where the series resistor is.
Heat is not a problem. You don't say if the "12 Vac" is RMS, peak, peak-to-peak, centered about GND (both positive- and negative-going), 0 to 12 V, etc. Let's assume one of the worst cases, that the signal is 12 Vac RMS, centered about GND.
With a fixed zener diode value, the power dissipated in the resistor and zener is set by the resistor value. Start with a zener value of 3.0 V. The input impedance of the uC A/D input is very high, and the zener diode does not conduct until the input is above 3 V above GND, or 0.7 V below GND. For a first-order approximation, we will average the two resistor voltages (9 V and 11.3 V) for a resistor voltage of approx. 10.15 V RMS-ish; call it 10.2 V
With a 1 K resistor the worst case power dissipation is just 104 mW in the resistor, and much less in the zener. A 1/4 W axial resistor will be barely warm.
Because the input impedance of the A/D is much higher than the resistor value, the resistor has very little effect on the signal amplitude seen by the A/D input when the zener is not conducting. For example, if the input impedance is 100 K, then the 1K resistor in series with it decreases the signal amplitude by approx. 1%.
Note - if the anemometer is a simple AC generator, then the impedance its output sees will affect how hard it is to turn, injecting an error term into the system. For this reason, the added series resistor should be as high as possible because all of the current going through the resistor when the zener is conducting comes from the generator. The sensor might come with a spec for a recommend loading value, or minimum load value, or something like that.
O O O O O K K K K K
After writing all of that, I read the Interfacing app note. On page 1 is the recommended interface circuit that has a resistor in series with two clipping diodes. A single zener diode will do the same thing as the two diodes they show. Because you already have a uC, A/D, and software that works at the lowest signal voltage, you do not need an external comparator circuit. You would need one if the sensor signal were going to anything that requires "a logic-compatible digital signal" such as a frequency counter or a digital GPIO pin, or but you are not doing that.
https://www.nrgsystems.com/assets/resources/an40C-IF3-interface.pdf
I'm not impressed with the tech data. I couldn't find a wiring diagram that shows how many wires go to the sensor and what they do. For example, if the sensor is powered and has an output signal driver rather than the bare generator outputs, that makes things much easier.