Well, in order to even attempt a debate, we'd need to set ground work for what constitutes a monster and what constitutes bad decisions (on the game players or bioWare's part).
Just to get the game stuff out of the way: The beholder dungeon doesn't really need to be cleaned out, you get the prize from the first beholder you meet. Conversely, you don't clean it out you miss an experience farm.
You, then, don't need to clean out any dungeon because Andalon will take you right to the door when you've brought your eggs to her. Even Andalon, (LG?) doesn't wipe them out.
Beholder, Kuo-Tao, etc, are more easily demonized because they seem to lack language. Ultimately, I guess, what makes a monster a monster is in lacking the ability to change; lacking reason, wisdom, and ultimately, capacity for compassion. Feel free to expand on or contract this - you bring up an interesting point.
Then, if we want to step outside the BG game world and view traditional monsters in a different light, et's start with the drow: The only thing we see in this drow city is adults. How reasonable is this? They certainly have children? They included a few examples of drow who did not feel as other, perhaps more wicked, drow did - Solaufein and Phaere, even the worshippers of Vhaerun and possibly Jarlaxe. They are all murderous drow with no capacity or capabilty to change, perhaps leave?
I can't even begin to try and get in the head of a beholder or illithid.. someone else is gonna have to take that one.
But one thing I will say - no matter how many times I play that through I still can't bring myself to corrupt that Kuo-Toan pool. That would effectively kill their race, as well as being an optional act.
Is this your attempt at gauging the reactions? I didn't realize that the PC gets a virtue increase for freeing Viconia, I assume they get a virtue decrease for letting her burn? ...what was the question again?