It could be a RL reference to the Serpent in the first chapter of the Tora and the Bible (I believe that chapter is called Genesis in english), the one who offers the fruit of knowledge to the fledgling humans. It's a big enough part of the cultural heritage of us westerner RPGers for FFG to use it as a reference. So if the Serpent is a symbol for someone who wants humans to have knowledge so they can make up their own minds about things, it is certainly so that the Inq would want to enforce the idea that the Emperor wants to kill the Serpent. It can of course be interpreted as a simple warning: "If you act like the Snake and give this information to the humans (=general populace), the Emperor (=Inquisition) will kill you".
You know, the 40k world is so twisted that even the Serpent can be made to seem like a reasonable fella :-)
I'm not certainly saying that it is a RL-reference, only that it might be.