It's the roads that lead to nowhere
That seem to draw the most -
Nice two lines, I feel like I've heard it somewhere else, but I don't know where. So I like it as something fresh.
Covered by consensual lies -
Consensual lies, interesting.
The conscience becomes a ghost -
As in there is no conscience, or it's hardly there?
Evil ascends -
Bah! I'd sure hope not!
When lost in words of advice
The belief becomes a law -
Alright, the lines are still nice, but now I feel like I'm being lectured to
Chartered by the martyred books
The passions burning raw -
Interesting
Evil ascends
'Cos God turned their hearts to stone -
Psh, well, it's your lyric 
See the masses come to pray
Scars that build the cost
Salt water is turned to wine
Raise your glasses to the lost -
Inferencing that the religious masses are the lost? I see some hints, but I feel the use of raising you glasses conflicts with the other things you propose. Toasts are usually positive.
Evil ascends
Evil ascends
'Cos God turned their hearts to stone
All in all, it's a nice lyric. There's a lot of thought in it, and a careful crafting of well chosen words. I would have liked to see more images, such as you used toward the end, to balance out the heavy lines of meaning, perhaps displaying them. Your style tends to embrace the vague, but I think it could still use a sort of clearing up in the mentioned areas.
