The red-green test (binocular balancing) does work on anomalous trichromats, i.e. most of the people who are colourblind or colour deficient. Just because you can't distinguish between red and green doesn't change the way the wavelengths focus. (We have to adjust our questions to refer to the right or left side, rather than the red or green, but that's about it.)
Very few people are missing a particular colour of cones; rather, the light-sensitive pigment is altered by genetics to be most sensitive to a different/"wrong" wavelength. So your red-green colour deficient people usually have their 'green' cones more sensitive to red instead of green (or vice versa). That doesn't mean that they don't see green, they're just less sensitive to it than they are to red; the photopigments are still activated by wavelengths other than the one they're most sensitive to.
For more info, look up the spectral sensitivity functions for the various photopigments; you can imagine how shifting the sensitivity of any of the curves will affect things, but it will in no way prevent normal colours from being visible.
(I'm an optometrist. And yes, it's spelled "colour" here.)
