Oh, the anti-Vulcan prejudice was there for a perfectly good reason. I just really thought it was clumsy and unnecessarily obvious - and it really seemed forced and unnatural, too. In a lesser episode, it might not have bothered me as much, but just about everything else about the episode is just so good that this flaw really stands out. It's not enough to spoil it for me. obviously.
In his novelization James Blish made it clear that Romulan bodies had been discovered which resembled Vulcans. That would make the connection pretty obvious. Of course, it would take the edge of the reveal of the Romulan bridge.
However, it took repeated viewings for me to catch on. The first time around I was so caught up in the story, that it didn't really dawn on me that Stiles had no real reason to believe that Spock might be a spy.