You have two choices in BG2, side with the Shadow Thieves or side with the Vampires.
The fact that if you side with the vampires, you still get betrayed by Bodhi proves that it is the 'evil' choice out of the two.
Shadow Thieves are not an evil organisation. In Fact Imoen is a thief and Neutral Good. Robin Hood would 'steal from the rich to give to the poor' as an example of a Chaotic Good act of thievery.
That is not to say that the Shadow Thieves are a 'good' organization either, however all that they are is that they are not a 'Lawful' organization, and would likely attract interest from non lawful good, neutral and evil aligned characters.