You are still able to progress the main quest even if Jake is dead (you will lack a journal update but thats it).
SPOILER:
After his death, you can pick up the amulet & choose to go kill braccus at the Church in Cyseal to the east (optional).
For the main quest, move north in Cyseal towards the fiery area & keep following the path, all the way up north there should be a bridge. This bridge leads to Luculla (which is where the journal update would lead you, if you spoke to Jake). From there onward you can pick up the main quest again.
