RGBRGB 2 pixels on a 2megapixel camera
RRGGBB 1 pixel on a 1megapixel camera

Interpolating from the 2 to the 1 will give a different average, BUT, usually the smaller pels are noisier so require more post processing.

Remember though, we are talking 100ths of a mm in either scenario.

Given the choice between 2 sensors chosen from the same factory and having to enforce both to the same lower mpixel range I would choose the lower mpixel one.

the signal to noise ratio of each pel is greater (larger surface, more light, more difference from background noise).