> I don't know if the waveform is suitable for the RTC
That's a good idea, but I'd guess the sine-wave wouldn't be suitable. Referring to "2.8 Clock Source Electrical Specifications" to find the required slew rate for the RTC_EXTAL pin, and find they don't give ANY specifications for this pin, slew voltage or frequency! There's no mention of any hysteresis on the input, so you can probably assume there isn't any.
You'll have to give it a 60Hz square wave.
I've seen devices that use a filtered mains sine-wave as a clock input start running really fast when there's some noise on the mains. Like the switching noise from a Motor Controller. Like you're building.
I'd suggest you SERIOUSLY low-pass filter it to remove all spikes and glitches, and then turn it into a square wave via a Schmitt trigger. You can use an HC14 or build something out of a few transistors if you can't afford the space or money for the HC14. You could use op-amps to do the filtering and the squaring. Circuit examples here:
Schmitt trigger - Wikipedia, the free encyclopedia
Tom