to those worrying about judging thoughts instead of crimes, that's an essential feature of justice. That's why there's a difference between manslaughter and murder. The intent in the latter makes it worse than the former.
That's why the attempt to hide behind "sex play gone wrong," aka "oh, soz, accident!" is so revolting as a cover for murder.
We read intentions all the time, and some really are worse than others.
The question isn't whether intentions matter. It's whether those intentions matter. Is torturing someone for belonging to a given class worse than torturing random human beings?
I'd say yes. It adds an extra layer of injustice to all the layers of pain.
And the other thing I'd say is if you can see why crimes targeted at Jews or Muslims or blacks are hate crimes, but you're dubious when it comes to women, then a) it's precisely to clarify the parallels that we need the hate crime designation, and b) take a long hard look at yourself.