Each of these options has its own advantages and disadvantages, I guess.
For #1, I would add that some MCUs have analog watchdog features which might be used to detect the zero crossings in hardware.
For #2, it is very hardware specific, but if you’re willing to settle on a MCU and pinout, then it can be possible to combine #1 and #2 as some MCUs like STM32 support the comparator feature in addition to ADC on the same pin.
For #3 I see it as being the least flexible, not the most, as you only get the digital comparator output on the MCU, and close the door to voltage measurement (which might be needed for more advanced algorithms) and software configuration of the setup. But it might be the easiest option to implement, and the only one that is truly portable to many MCU types, so its most flexible in that regard.
An option you did not mention is the use of dedicated voltage sensing parts, some of which are available with optical isolation, perhaps because of the high cost?
Another option might be some op-amp buffers for the voltage and centre tap, even if not isolated, to have a nice low impedance signal to measure and a bit more isolation between MCU and motor.
I am super-interested to see the result, whichever way you decide!