I personally would not consider this negect to be benign. I do think that it is justified given how little money there is for corrections and how many men are incarcerated, but I would not think say that it is benign.
The reason I say this is that women end up undergoing punishment that is more severe than a simple prison term would be. For example, as the link shows, many women are sexually abused by their guards in prison. They have been sentenced to prison, not to sexual abuse. Allowing the sexual abuse is neglect, but it is not benign. The same goes for the lack of medical treatment mentioned in the link. Their punishment is supposed to be incarceration -- not deprivation of health care.
Since we incarcerate so many people and do not want to pay for it, it is easy to see why women are neglected. That does not, however, mean that the neglect is benign.