I think Upsettingshorts puts it quite nicely: malice and callousness are not the same thing, and I see Morrigan as coldly calculating more than evil. Dire threats require sacrifice to overcome, in her estimation. Notice how she usually tries to get you to dismiss or sacrifice people who lack useful traits or social significance, but will defend those with unique circumstances or backgrounds. Is this evil, or saving what must be saved? Morrigan sees people only for what they presently are and not what they could be; realism divorced from idealism is unfulfilling and self-defeating, but not intrinsically evil.
Compare this with real world debates, especially ones regarding espionage, torture, rules of engagement, personal privacy and other national security questions. Would you call the people you consider the be going too far to be evil? Or, more likely, would you call them misguided? (Please, no specific RL examples, don't send this spiralling off-topic...)
I know people knock D&D morality, but Morrigan as true neutral makes a lot of sense. She doesn't go out of her way to harm others, but will do so in the furtherance of a worthy goal. To kick it old school, if the conniving Saemon Havarian of BG2 is True Neutral, then Morrigan has no trouble qualifying.
Ironically, ME2 and DA:O gave people evil LIs-- I'd say Jack and Zevran qualify. The problem is, BW writers know players like to try to reform evil people, and so they tend to use psychological trauma and other external factors imposed on evil characters to justify their behavior and make redemption seem possible. Viconia, of BG2 and one of my favorite bad girl game romances, also fit this bill.
Bioware can't rely on these inhibitors while making someone truly, deeply evil. If they did want an evil "that goes to 11," I think they need to go beyond chaotic stupid and make a deeply intelligent and disturbing npc. The most evil villians are always the ones who destroy moral compasses, who can make any decision seem destructive, self-serving and futile.
That kind of villian as an LI would be awesome, but very difficult to achieve. They'd have to seriously have a shot at corrupting the player, which requires subtle writing and difficult choices.
I guess I'm saying, if they can pull it off well, sign me up.