There are two ways to approach the above:
Spoiler for Spoilers up to episode 3 of the anime:
Assumption A: The murders are carried out by means of witchcraft
This would make them impossible to stop by ordinary means and explain a lot of the incredible stuff that has happened so far and is bound to happen in the future (sadly, it would also mean trying to use reason to deduce what happens next is pretty useless).
In this case, as you noted, the witchcraft-literate Maria would be capable of interfering e.g. by handing out scorpion charms. If we assume that Natsuhi was the proper sacrifice and somebody else was chosen, wouldn't it be possible that the replacement was the person "next in line"? Basically, Shannon's death fulfills the condition of the second twilight, and does it better than the simultaneous death of Eva and her husband. This could mean that Maria's interference accidentally messed up the proper order of the killings to the point where the game may be impossible to solve properly, just like the worlds of Higurashi where Keiichi didn't transfer to Hinamizawa at all. Of course this would be a nasty thing to do in the first chapter... but who knows.
But less complicated is the other option:
Assumption B: The murders were carried out by conventional means only.
In this case, Natsuhi's survival appears not to make sense... until you flip the chessboard. The murderer has already "created" Beatrice by writing the first letter, now they act in ways allowing them to maintain her existence - that's why there was that occult circle (recognized by Maria, meaning the culprit is deeply knowledgeable about witchcraft) on the door. If that person saw Natsuhi receiving the pendant or found it in her room before murdering her, it would make them not want to kill Natsuhi, because anything that discredits Maria also discredits Beatrice. However, if that person were to make it seem as if the pendant was the only thing that saved Natsuhi, the Beatrice theory would gain additional points. Shannon would get killed to fill the six people quota required to upkeep the image of the curse.
The fun part is, the murders would follow the epitaph regardless of which of the above were true. So it's a preview for us right now. I don't think it'll be possible to solve the message behind the epitaph for us anime viewers for quite some time to come, though.