For distinguishing between red and green hues for some people, http://colortest.it/enhance-r:http://brilliantmaps.com/the-g... might be useful (or the "Enhance green" setting, or switching between the two).
would it be so hard to put the short one/two/three letter haplogroup names from the keys inside of the largest slices? or to show the pies consistently with the same groups in the same order?
It's not that hard: if you need to distinguish a small number of colours, make them sufficiently different in luminosity: if you wouldn't be able to tell the colours apart on a greyscale photo copy, someone will be unable to use it. If you need to distinguish between a large number of colours, use additional clues (e.g. labels, patterns, etc) other than the colour itself.
It's not "not easy to distinguish between all colours". It's impossible to distinguish between some colours, making the map itself meaningless. This is akin to having a heatmap where the "hottest" and "coldest" areas are indicated with the same colour: the result is useless unless you're specifically interested in "average" vs "extremes" (with no regard for direction).
I'm not even colourblind, just colorweak and I am fairly sure there must be some set of colours that are both differentiable and looks ok at the same time.
Alternatively here's a feature idea for someone who creates charts / chart toolkits: make several palettes, including one with safe colours and/or hatching.