Having watched the film in the midst of readying things for a trip up north (FRENCH '21 continues with "phase two" on Friday evening), I can say that what happened to the female victim and the actions of her father (played by the aggressively typecast James Cromwell) were indeed unspeakable. But the fact that such vicious crimes do happen against women doesn't necessarily make a film centering on such horrific acts into a top-flight work.
Some of the critical pushback came from those who were uncomfortable with the more graphic depiction of said events. Others questioned whether the filmmakers were having things both ways, as in the following comments from critic Russell Smith of The Austin Chronicle:
Overtly, The General's Daughter argues that men's screwed-up, hypocritical attitudes about sex are to blame for restricting women's horizons and poisoning their sexual psyches. On the other hand, almost every withering attack on said hypocrisy is undercut by a gratuitous, lingering image of Elizabeth's luscious naked bod spread-eagled helplessly on the ground or writhing beneath a faceless, implacable rapist. Bondage porn for self-loathing pervs, you might say. Like the “classy” men's stroke magazines of the Sixties, The General's Daughter inspires all kinds of cognitive dissonance with its blend of high-mindedness and cheesy titillation. Very odd, and very icky. Highly recommended for graduate psychology students in aberrant sexuality, but others can probably skip sans regret.
I think a counter-argument can be made to these critics about the film's overall intentions, but I'm not sure that vindicating the film from the critical objections raised by Smith and others will reclaim it for a place high in the pantheon of neo-noir.