Dragon Age: Origins uses an approval system with its followers that is point based and displayed on something like a number line or number ray (not sure what the right word in English is), lets call it approval bar. With changing values the reaction toward the character changes. For positive changes the follower is more open to the player's ideas and with negative values it is possible that the follower would leave or even turn hostile.
Using that system for my own mod is something I will try to implement. The basics are there but effectively tied to the original followers from Origins. So far I can change the simple point values and get the value via script. To use the whole range of options available I have to dig a little more, make copies of more core scripts and adjust the system to my followers. It is a bit of work but would be nice to have in the long run.
As for having something like a "morality meter", that is a little bit more complicated. I would like to have something that the player can see in the GUI without searching for it. After some experimenting I found out that I can also enable the approval bar for the player character (pc). It easily fits into the GUI and the values are handled the same as for followers (no surprise there, its the same system). But the player won't know that this approval bar is different from the others and changing the icons just for the pc doesn't work, it is a part of the GUI that I can't edit.
Another idea came from another modder in the BSN toolset forums that suggested using items as tokens for a reputation system she uses in her mod. These items would be assigned as plot items to not count against the item limit and to be in a separated section of the inventory screen. Using those tokens for different factions as signs that you had dealings with them is quite a good idea when the core game had nothing to represent factions in the first place like other crpgs have.
Combining the pc approval bar with tokens for morally wrong decisions could be just what I wanted. If the pc passes a specific value on his/her approval bar a token is put in the inventory and by the description of said token the player can see if the consequences are worth the action. I will not make these tokens a bad thing per say. They will have consequences both beneficial and limiting. For example there could be some talents that get unlocked that mirror the decisions previously made but at the same time some npcs might not want to have dealing with the pc anymore or even turn hostile as a result. There will be ample warning of mayor changes both in the mentioned token descriptions and by journal entries that Ben makes.