I see what you are saying, but the problem is that this is not consistent in all games. I would expect this kind of thing more from older Adventure games, where gamer's hands were not being held as much as they tend to be with modern games.
With most modern games, and indeed, even AG's, the gamer is expected to exhaust all possible dialogue choices.
Indeed, the politics going on in Risen, and the fact that certain dialogue options could land one in hot water, is a feature of the game that is partly expressed in the system you describe, - but how is the gamer to know this, beforehand, especially at the beginning of the game, where the politicking has not become clear yet?
A little warning as part of the tutorial /loading screen tips could have been added , or a little warning regarding this in the manual, and everybody, including you and I, would have been happy.
It is a sad fact though, that modern gamers have been "trained" to exhaust all possible dialogue options, and I think it is from this situation that confusion stems with this feature of Risen.
I do remember some of those old AG's where the very outcome of life or death often depended on your next dialogue choice. In fact, I actually applaud such a system, (makes things a lot more interesting, and forces you to think a bit instead of just dully clicking your mouse) but if that was what PB was aiming for, they should perhaps have polished the implentation of it slightly more, and been a bit more upfront with it, in order to avoid confusion, since these days, a lot of gamers are not used to the idea.
Not mentioning it at all, as for instance, part of the general tips and hints they have scattered around in the manual and loading screens, runs the risk of it seeming like sloppy programming, as had been my first impression.
Something like: "Careful of what you say to people. Not all dialogue options are always the best one." or: "Careful of which dialogue options you choose. They don't all have a positive or desired outcome."
I know this should go without saying, but we are in 2009, and, well, I don't want to start a mudslinging match about what has been going on with many games these days. *shrug*
Anyway, there is a slight subtle difference between to have to choose between one dialogue option, or another, and the dialogue options simply not making sense.
For instance, me telling Brogar that I took the piece off him after defeating him in the ring; while in actual fact I had pickpocketed him, really does not make sense, and that is something your character just says; it's not one of those "either/or" options.