I've been having trouble inserting moral dilemma into my campaign as well.
3 issues have come up: 1) my acolytes tend to function on a self preservation first, morality second pragmatic mode; 2) they often tend to act w/o taking time to get complete information resulting in the only moral question left afterwards is: do I feel guilty?; and 3) most recently they accidently by-passed the moral dilemma.
1 - should be self explanatory w/ no need for examples;
2 - One of my acolytes is an arbitrator, and in a recent session he temporarily was granted command authority over a wing of thuderbolt fighters loaded out for ground-strike capability. The cell was aboard an aircraft near a ground engement in which a noble's private army was exterminating a thousands strong bandit faction (in the bandits home-territory). The acolytes needed to talk to the noble, but he was commanding in the field and though it was clear his forces would win due to better numbers, training and gear, the best estimates was that it would take all day and into the night to finish up the battle. The acolytes didn't want to wait that long, so the arbitrator ordered the fighters to attack the bandits. Two bombing runs (each fighter carried 4 bombs) and a strafing run later, the battle was over except for mop up. The acolytes landed and went to talk to the noble. Watching his men pile the corpses of the enemy they discovered that the noble's army had been attacking the bandits main home-settlement. There were neatly sorted piles of women, children, old folks and pets to go along with the dead fighters, more than half of which were wiped out in the airstrikes. Looking at piles of dead children's arms and legs made the arbitrator feel guilty about ordering the bombing, but by then it was kind of late to make a better (or any) moral decision.
3 - I set up a scenario where the acolytes would run into some mutants in a massacred settlement in the wastelands. The idea was the acolytes would tangle w/ the mutants thinking them to be the bad guys, then find out that the mutants were escaped prisoners from the real villians the cell was after (who were human mercenaries) and have to decide whether side with or kill the mutants anyway. Well, the characters unfortunately decided to do extra fly-bys over the site they were investigating and as a result got shot down. Due to injuries, they then decided to hide and wait while sending one scout to look around. This resulted in most of the cell tangling with the returning mercs before they ever saw any mutants, and by the time they ran into the muties the acolytes were in full flight from overwhelming force and willing to take whatever help they could find no matter how many eyes it had. (see 1 above) so no moral dilemma of thinking someone was enemy then finding out you were wrong. They basically stumbled around having to make the choice.
So as I said putting moral dilemmas into the game has been tricky so far.