Actually, I agree with you in cases where impulsive crimes like manslaughter or provoked assault are prosecuted as hate crimes. That's like saying one dangerously irrational predisposition may be better than another equally irrational predisposition even when they have the exact same result.

But when the crime is planned, then distinguishing them based on the amount of thought put into it is a natural extension of what we already do:

Manslaughter: "I was then pre-disposed (given who, when, why, where, and how) to now kill X."

Murder: "I was then pre-disposed (given who and why) to then gradually plan (filling in when, where, and how) to now kill X."

Murder Hate-Crime: "I was then pre-disposed (given why) to then gradually plan (filling in when, where, and how) to then gradually plan (filling in who) to now kill X."

If planning to kill someone given the chance is more criminal than killing them without malice aforethought, then surely planning to make such plans given the chance is even more criminal than that. You can take "more criminal" to mean "less likely to be a one-time event," "harder to rehabilitate," or even "invoking vengeance from a broader group of affected people." Whichever you pick, it makes sense that the more open variables in the planning process, the more criminal the chain of behavior as a whole.