I've followed this discussion and I have a few things to add.
Personally, I can see an argument for both sides. Lets start with an analogy similar to Jester's...
First lets assume you're in a committed (romantic) relationship with some significant other. Imagine you are having a lucid dream (wherein you are aware you are dreaming and can direct the course of the dream, or at least your own actions in it) and the extremely attractive person of your choice is coming on to you. You have the choice in this dream to either sleep with this person or not. Honestly, would you feel obligated to refuse the offer? And just because you may make the choice to sleep with this person in a dream doesn't by any means infer that, were the opportunity to rise, you would sleep with them in real life. This is because in the dream there are no consequences whereas real life actions do have consequences.
However, from a strict RP-ing point of view (that is, from the point of view the IN GAME character, not the actual player), it's arguable whether or not the PC has the awareness necessary to surmise that there may be more to his/her Irenicus dreams than simply... well, dreams. If the PC does have the insight to realize that these dreams are/could be significant than I think a virtue drop is appropriate if (s)he makes the more "evil" decisions. However, if you imagine yourself in the place of the PC, you may not have reason to believe that these dreams are anything special (which, in the original game, they're more or less not as far as having any consequences). In this case the only solution I can see would be some kind of wisdom check on the PC done by virtue to estimate whether the PC would forsee possible consequences of his actions in the dream before changing virtue's value. But I don't know if that's even in the scope of the mod and i'm fairly sure it would not satisfy all players.
In the simplest terms:
Wisdom < # = no penalties for either evil or good choices
Wisdom ># = virtue penalties for evil choices
On another note, if one main objective of Virtue is to influence your party members' "happiness" then I would say that logically virtue should almost definately not be affected by the happenings of dreams because unless the PC tells his/her party what (s)he said/did in their dreams it's very unrealistic to suspect that they would know and think less of the PC because of it. I'm sure that's not Virtue's only goal but as it stands the way it deals with the issue at hand seems a bit discontinuous.
Hope all of the above made sense.