I've seen the following argument several times in recent months:
1. Hate crime laws make a penalty more severe only because of a different intent.
2. If you increase the penalty for a crime merely because of the motive, you are criminalizing a motive, i.e. a thought.
3. Therefore, hate crime laws are really criminalizing people's views and thus are thought crime laws.
The result is that a number of conservative organizations have been resisting hate crime laws and calling them thought crimes. Family Research Council is one group that has been doing this. When Congress had a bill on hate crimes in front of them, they were sending daily emails calling the bill a thought crime bill. I thought it was inaccurate to label it that way at the time, and I'm even more convinced of it now after reading Eugene Volokh's post from a few weeks ago on the subject. Volokh points out that we do this sort of thing all the time, and no one has any qualms about it. Treason is a thought crime, on this view. If I stole a government document in order to destroy it for the fun of it, it wouldn't be treason. But if I did it to sell it to North Korea or Iran, it might be treason. Also, murder or manslaughter can differ in terms of intent, as can different degress of murder from each other and different degrees of manslaughter from each other. Intent is extremely common as a means of distinguishing between different kinds of crimes with different penalties. Even less controversial discrimination laws can distinguish between different penalties (or whether a crime has even been committed) according to intent.
If those things count as thought crimes, then we shouldn't be opposed to legislating against thought crimes. But I think it's probably better to recognize that none of these things counts as thought crimes. A thought crime would be thinking something without doing anything further and then being arrested merely for having the view.
I haven't said anything about whether there are good reasons to favor or to resist including sexual orientation as specially protected in terms of hate crimes. I think there are reasons offered on both sides that have some merit. But it's silly to oppose these laws simply because they treat two murders or assaults as different according to motive. It's true that both are assaults, but they do have different moral factors that apply to them. One is a worse assault. At the same time, we don't always recognize morally important issues as affecting what kind of crime someone committed or even whether they committed a crime. I'd love to try to think through (at some point, not today) which factors count as legitimate ones in terms of motive. But ruling it out merely because it does involve motives is at best ignorant of how law generally works in this country with regard to different motives for the same act.