Yeah - that would work, although you would need to impose the same rule on Samael.
Also, maybe once the artefact has left the game, there are no longer any penalties for fleeing - after all, your people have completed their mission, and sticking around would be a bit daft. It would also lead to a bit of a scramble as the side with the artefact tries to leg it, while the other team does everything they can to stop them in their tracks.
Maybe you could introduce some special rules to make the artefact a bit "killy" (+1/+1 or something better), so that when you are in control of it, you have a tactical decision to make - do you leave for the VPs, or do you stick around to use the artefact (but risk losing it in the process)? If the artefact was "killy" it would also even up the score for Samael, who risk losing a character on the very first turn from the traitor attack.
The VPs for the artefact might also be higher - as far as I know, the lowest cost character is 35 levels, and I am not sure it is worth sacrificing 35 levels of killing power for 25VPs. If the VPs for the artefact are too low then the game might just turn into a head-to-head annihilation game rather than a proper scramble to seize control of the item.
Sorry - I'm just kicking around ideas because I like your idea of a team of Church purists bursting into a dark cellar to bust up a coven - it's very Lovecraftian, and it plays out nicely in my head