I don't care for morality system in games because morality and emotions in general are fundamentally illogical and highly subjective, it is not something that can be quantified with points.
I think you should be able to make your character look however they like, and independently characters react rationally. For example you can murder all the people from town A but reward people of town B... you're still evil for all the murdering but people of Town B won't cower from you. Good and Evil are relative things.
I mean I morph my character into an angelic and serenely calm being, but how is that possibly a counterbalance if I kill defenceless NPCs without provocation, just for fun. Hell, the angelic persona may just make my character seem more evil, like the sadistic priest played by Lee Van Cleef in some Spaghetti Western, or a cruel avenging angel.
I think if there should be any points they should not go onto YOU, they are not for YOU to carry around. Evil people don't know they are evil, evil is defined by how OTHER PEOPLE around them.
So I say if there is any morality system it should not be focused on your OWN stats, but on the Stats of NPCs. Like in the OP's example, your stats should not change by how you treat Tali, but Tali should change his/her stats on how (s)he sees and thinks of you.
It is easy to pin those stats to just the playable character but that is the huge logical flaw, your moral position is a product of people around you that develops while they are out of contact with the playable character, when the game wants to just free up the memory space from that AI.
It's interesting how many game developers treat your playable character like many churches treat "sin" of individuals - the "wrongs" they have done - a mark on their own character that is somehow universal for all and not subjective at all.
But this is very distinct from personal guilt, pride and happiness, but the game cannot hope to give or subtract points for that as those are innate feelings that the developers have to inspire in the actual players through the ART of the game itself. Yes, that's right, inspire an emotion other than excitement of competition, can video games do that? I'd call that a requirement of the "games are art" thesis.
If the player just doesn't connect with the characters in the game, that won't necessarily break the game as your character could just be a psychopath i.e. has no emotional connection with anyone in their world, and is only interested in personal material gains. They are only ever nice out of self interest to avoid confrontation and earn cooperation.
I mean really, what IS the difference between playing a realistic video game and being a psychopath in real life? I know almost everyone has at least once gone on shooting sprees through Liberty City, not because they hate the inhabitants but because there is no human connection. They don't feel they are depriving human life, they are so transparently simple robots that only vaguely act human.
So that's my idea of a morality system:
-Let me make my character look however I like, regardless of how "good" or "Bad" I am behaving
(Important lesson here is just because they look good, doesn't mean they are)
-Don't apply moral or emotional stats to my Avatar, it is just an empty shell I am inhabiting, only physical/magical attributes
-Any morality points system should be applied to each NPC and how they view me a mixture of rationality and emotions
-the sum of my NPC interactions add together over time as rumour spreads through NPCs, like if I am more cruel to a particular group that group may either fear my character or join together to confront me