AVR ADC can measure rms?
If you want to use an undocumented feature then that's fine but if you want to be safer you need to calculate RMS based on the input waveform being fully within the upper and lower limits of the ADC. 

You also need to take enough samples per second so that your RMS calculation fully takes account of harmonics in the waveform.

Removing part of the waveform is OK provided you are dealing with sinewaves (no harmonics)  and you take account of this "planned" distortion.