Clifford LB Hubbard's Dogs of Britain (1948) mentions that the Pekingese was used as a pet by Chinese royalty, but not its use as a guard dog. Here is a neat piece from 1974. It gives a pretty interesting history of the Pekingese, including its use as a royal pet, but does not mention its use as a guard dog. The American Kennel Club also prepared a small bit on the Pekingese; it's less extensive, but it corroborates the fact that they were royal pets, and also does not mention the Pekingese' use as a guard dog.

According to one account, the first Pekingese dogs to arrive in England were found by British soldiers storming the Summer Palace in 1860. The dogs were surrounding the body of their previous owner (allegedly one of the aunts of the emperor). Other accounts state that the dogs were found abandoned. It's possible that the story of the Pekingese standing vigil over their deceased owner is the origin of the "guard dog" story.

Given that we don't seem to have any written accounts (at least in English) of the Pekingese being used to defend the emperor, I'm inclined to think that this a fanciful legend. However, I would be happy to see any evidence supporting the premise of the original question. If my post has veered into the area of speculation or inappropriateness regarding the standards of /r/AskHistorians, I sincerely apologize.