You make a good point, DAD, that seemingly smaller, unrelated events do play a part in the bigger picture. One thing I always noticed with all the walkthroughs and such is that restoring Mardenus' sanity is not considered a vital quest. It's seen as a good introduction to the game play and a chance to level up, but optional if you want to get right into it.
So how does an insane Mardenus join the Council of Seven?
The necromancer, Theolin (name?), is also used later in the story where the grave robbers are collecting parts for him.
All these small things (if you can call a mage posessed by a dead necromancer small) do tie into the bigger picture. It doesn't have to be obvious, it just has to be.
The only thing that really bugged me with the Divine Divinty story line was "The Source." After having the healers complain about it for so long at the start of the game, it just seemed to vanish. No explination was ever given, even after defeating the Demon of Lies.