Update...
Why do some seem to be assuming I have a hostile or negative view of the player's actions or that I'm "out to get them"? I'm simply trying to find out how their actions affect their alignments, I'm not judging their actions as negative or positive. If I had wished to decide rashly, I wouldn't have bothered posting here.
In D&D alignment is not a relative thing that can be explained away by motivation or any other relatavism. If their actions change their alignments, that's not a "punishment", it's simply the character growing and changing over time. I've noticed a bit of hostility over the idea of changing alignments, as if it were a punishment to the player. Is the player role-playing? Yes, damn well actually. Can good role-playing lead to alignment changes? Why not? Why is this a bad thing?
Personally, I'm all for characters changing over time. I can't imagine people going through what adventurers go through and not be deeply affected in their world views. I try to support and reward such things whenever possible in my campaigns, not punish them.
D+1, as far as my use of the word "commands" for the monk, I used it because that's what he did. The monk told those characters what they should do. He told the sorceress "Take care of the doppelganger.", and told the dward "Secure the room." Those are commands in my book... and does he have authority over those characters? No, the group is more or less democratic, but at this particular stage of the game the monk was asking many of the questions, and more or less "leading" the party.
As far as my decision on the events and the affected alignments, here is what I've concluded (though our game isn't until Saturday, so there is still time to change my mind on this if need be). A single action, unless extremely hineous, isn't enough to change alignment. Most of the actions taken, though not clear, aren't enough to begin an alignment "shift" (I'm using shift in the sense of leaning towards a new alignment, not actual alignment change).
Before last night's game I had made a decision. If the rogue chose to assassinate the doppelganger, his road towards evil would begin. This doesn't mean that he turns evil, or that I'll try to influence his actions. Only that the "evil" path would make itself more obvious and certain events would transpire (such as the rather nasty idea by John Morrowto have the main bad guy assassinate the rogue's of girlfriend to push him over the edge). What path the rogue takes is completely up to the player, but the path towards evil is well paved and easier to traverse then it would have otherwise been.
Well, now for an update on the events that transpired last night. I DM'd the mini solo-game with the rogue... He ran to the home of his girlfriend to find that her and her family had left the city to take a tour of some properties they owned in lands to the south (Tethyr). He used a Qual's Feather Token (Bird) to send her a warning and begun investigating the whereabouts of the doppelgangers. He finds that their leader, the one he stabbed, has been taken to a Watch precinct and is being held there for questioning in the morning. The rogue skillfully breaks into the precinct and after a tense-filled game he finds the creature asleep in it's cell. He assassinates it and flees from the site, loosing his persuers through magic.
What happens next, how will the other characters react to all this (especially the LG monk), I don't know... but this Saturday we'll find out. I'll post an update after the game.
Again, thanks to everyone for all the comments and advice, they are all welcome and keep them coming

. Thanks!
-Arravis