The most interesting part about the OP was the desire to turn the Morality Roll away from the random D10, and to using the FFG dice system. I kinda like that idea, but how to go about making that happen. The base dice are weighted toward Light, rather than Dark, and we need to include the conflict earned into the roll, WITHOUT allowing characters to game the roll.
To me, this means the "Light" side dice (Green, Yellow, Blue) are a fixed roll, EVERY time, SAME number and kind of dice. While the difficulty (Purple, Red, Black) vary depending on the Conflict earned. Maybe take the Blue/Black to be Roleplay related dice (give them black if they portray dark side tendencies, give them blue if they portray light side tendencies, hell, give them both if they do both).
Just to throw out numbers, roll GGY. This is generally professionally proficient in the system. This level of skill can handle most tasks associated with a given profession at average difficulty.
Now we break down the Conflict to difficulty dice:
1-2 : P
3-4: PP
5-6: PR
7-8: RR
9-10: PPR
10+: PRR
Then roll the pool. Success = +2, Triumph = +4, Advantage = +1, Failure = -2, Despair = -4, Threat = -1. Add together, and adjust Morality. This way, the roll may "succeed", but the player still drops in Morality because of all the threat he generated or something. Gives it a little more variance, and probably will not give large swings (though it still can).
Literally, this is my very first thought on the idea; please lambaste this and chop it into little fishies to see where things go bad. I have not done numerical analysis or anything like that on it...
Kevynn