Gosh, Tough topic, not sure if I'm stepping into hot waters but I'm gonna try to keep this nice and clean.
No, because of the obvious reasons. I would not consider any action strictly 'good' or strictly 'evil' because it is a very vague description of the event if I has an Idea for a "choice" system It would go a bit like this.
Religion A is a faction, factions have several groups:
Templars
Priests
Skeptics
Common
Each group prefers a different approach and shares their advantages and disadvantages for example, lets say Templars prefer a direct approach, attacking a problem head on with Sword, Heavy Armor, and Holy Radish in hand, whilst Priests are more Traditional and will approach problems according to customs or politics. Skeptics don't have much of a head for tradition but do not enjoy being lied to about or kept from any important information regarding their beliefs, and Common Chapel-goers are influenced by whichever of the 3 are in power.
Lets say the player character performed a quest for a townsman to retrieve his blade from a nearby cavern,and after further investigation, you discover a document that can damage a certain Priests reputation, which you then sell to the local post.
While you have a bit of gold lining your pocket, the priests don't like you very much, but the Skeptics are the dominant force in town.
Priests Influence = 3
Skeptics Influence = 4
As a result no change to the "Common" disposition was made as the quest had no effect on the Skeptics, but lets say that the story brought the priesthood closer together, as they can relate to the scandalous priest, causing them to be more well known and, over time, more influential.
Priests Influence = 3
Quest influence = Priests + 1
Priest influence = 4
Skeptics influence = 4
Templar influence = N/a
Common influence = N/a
A small-to-major power struggle, Major/Minor property damage, Priest-Obeying Shopkeepers become more competitive with Skeptic-following competitors and side quests for dominance start where the player can help one side subtly without damaging the other side, cause one group to rise to power by purposefully damaging another's, reputation, Cause another group to rise from the conflict (Zealots, Scholars, Templars, Hired thugs etc.) or simply leave them be and let them settle it.
As much as I like the idea personally I could be wrong about it, and Bethesda seem to be doing just fine without trying to stuff an elaborate master quest system into the game before it's release, still with what they have done with their franchise, I seriously doubt Skyrim will be a disappointment and that it will be worth our money, with or without a Karma system
(...but seriously, no.)