There are three fundamental reasons why I'm very hesitant about what is being suggested in these last replies.
First: Having cumulative actions over a prolonged period leading up to a massive disadvantage situation is (at least from my perspective) a lot more player punishment than having observable and incremental effects that gently remind us that this path is not without consequences. (I too am very firmly against punishing the player, but it seems we have different ideas of what that constitutes.)
Second: DOS2 is slightly niche, but it still attracts a fairly wide swathe of player types. We seem to represent the more hardcore roleplayer side to these players. Others don't really care much for this aspect of the gameplay and will just make choices based on what benefits them strategically. The game must be made and balanced with both of these groups in mind. The only practical way to do this is to make combat mechanics more or less self-contained, and keep every interchange between that system and the roleplaying aspects on a tight rein, so that it can all be kept in balance regardless of which aspect of the game is more interesting to a given player.
Third: There is a huge amount of hidden complexity behind the scenes in a game like DOS2. Managing this complexity and not letting it getting out of hand while still giving the player the impression of choice and effect is a large part of what makes developing this type of CRPG very difficult.
As soon as you start mixing variables and elements between otherwise separate systems (such as combat and dialogue role-playing) that complexity grows exponentially. This forces the developers to spend hideous amounts of time on balancing and managing choices---time that could otherwise have been spent on adding more content that would have a much stronger impact on the player experience. This doesn't mean that you couldn't have dialogue situations based on "karma"---they just need to be made separate to the combat system and thus be balanced within the role-playing/dialogue side to the game.
As for why Source magic is so powerful, my impression is that it's to separate it from "normal" magic. There must, after all, be a good reason why Sourcerers mess with the stuff, considering the disadvantages.
