As the Frenchman said when someone said there was a difference between men and women, "Vive la difference!"
As has been stated many times (both here and in the courts), there is a difference between race and sex.
Why does the NCAA have a different size basketball for women than men? Because the women want to be able to do some of the same things that the men can even though they have smaller hands.
In the end, the difference in handicaps is moot because you can always adjust a man's handicap to be "equal" to a woman's by changing it based on the course rating differences. So it is moot.
If it allows women to more easily compare themselves with the "best" woman golfer what is wrong with that? If one system was used, a woman could compare herself to the "best" golfer (almost assuredly a man), but not to the "best" woman golfer. Most women golfers play golf against other women in serious competitions. They want to be compared with them, not men whose games they are not familiar with.
A woman can establish a "man's" handicap just by posting using the men's course ratings. This is required for a female amateur who wants to qualify for a USGA non-woman's event I believe. In other words, if you want to try to qualify for the US Amateur, you must have a 2.4 or better index under the men's system, not the women's.