Yeah. TBH I liked the way DA:O handled things. It didn't have a morality meter, it just had your relationship with each party member, which could have done with extending to entire factions but W/E.
You are offered choices in what to say, or what decisions to make throughout the game. Things react. You're mean to your party, they don't like you and they'll either leave or just not say that much to you. You pick one side in a main mission, enemies from the other might try to attack you. Its still possible to game the system, but its not quite as easy to do so, and its easier to just play along.
There is no good or bad ending, merely the results of your actions are told to you. People went off and did things, you died or did stuff, factions did stuff, end.
If you must have a good/evil bar though, there are a few simple things that IMO should be done:
1. Don't tell people what is good or evil until after the choice, then hit them with a +20 a**kiss or +20 a**hole notice [Or whatever your game's equivalent is].
2. Don't have good/middle/bad endings. Just take note of what the player's choices effected, and note them down. No "You were just mean enough by being rude to everybody that we think you're going to try to take over the world", or "You decided not to kill innocents, that means you must be wanting to adopt all the orphans in the world and bring them up". Just tell the player what they're actions were, and what they effected. "You killed King X. His empire was cast into turmoil until his long lost son Y, who you found in Z, ascended to the throne", only more creative.
3. Have gameplay effects not tied to the morality system itself. I.E: Not like Mass Effect. In Mass Effect, you got Para/Rene points so that you could get Para/Rene options that would net you Para/Rene points. There Para/Rene options were also the only way out of things sometimes. Instead, do it more along the lines of KotOR or something. Your morality nets you bonuses to certain powers or skills, but it doesn't lock you out of options at points. There's no "You must be level 10 Evil to get past this point without a party member dying/leaving you". It effects the game, but it doesn't lock anything out - hell, from memory even the other morality's powers were available to you, they just cost more to use.
4. Have neutrality viable. Have it as a middle ground between good and evil bonuses, its not that hard. In KotOR, Neutrals didn't gain cost reductions for using one morality's powers, but they didn't incur cost increases for the other morality's either. This meant they were able to play as a more all round class. In Dishonoured, there are skills revolving around killing, and those revolving around stealth and passiveness. Were they locked to a morality, having neutrals able to gain the low-mid skills on both sides, and have themselves be versatile, whilst having strong abilities for each morality that neutrals couldn't get, but were heavily weighted towards one method of play [Stealth or Combat], then that would be the way to go IMO.