The Identity Crisis story is an epic win no matter how you look at it.
I think the criticism was directed more at how rape is used to give a female character deeper, edgier and all round more interesting. They never really criticize Identity Crisis; they just say it made DCU a darker place which it did.
It did make the DCU a darker place but I think it brought a level of writing maturity that was much needed. I see the success of it in terms of what it did for the League member's characters.
The rape itself is a difficult thing, no doubt. But I think the end result opened up a lot of writing options that would have otherwise gone untapped.