She's not racist, she's just not getting trapped by common sense!
I get what you're referring to there, but let's look at this:
While Sanae is polite, if not friendly, with humans, youkai she looks down on with contempt, and takes any opportunity to destroy them. The dialogs from UFO and 10D underline her utter lack of regard for them.
Reimu, another shrine maiden but one with vastly more experience in Incident Solving, while believing that youkai need to be kept "in check" to protect humans, at the very least counts some youkai among her friends.
These two facts about these two shrine maidens leads me to believe that maybe Sanae just has a lot of growing up to do, and when she gets to Reimu's level of experience, she'll come to realize that humans and youkai are equally tiresome and troublesome.