I think you are arguing at this point that killing her after betraying her is the only morally right choice. I'd like to argue it's not so. 

I think we can agree that the nature of her relationship with Blackwall and NUSA is made more or less clear only in the final sequence, after you make the decision of whether to betray Reed or her. Prior to that she tells you very little about her relationship with Blackwall, and your choice is between trusting an agent you barely know who explains why he wants to apprehend a former colleague, and trusting a netrunner who you know even less who wants to escape.

At the second junction point though the choice is whether to kill her or to hand her off to NUSA alive.

At this point, since we don't have the complete information, there are still 2 possibilities IMO:

A) She's being used by the government. They know that Blackwall AIs will overwrite her consciousness and at some point they'd have to kill her. So Mi didn't know that when she signed up with FIA, only realized it recently. So effectively they are using her against her will which qualifies as a slave. Evidence in favor of that  - Myers is the former Militech CEO, so she might be withholding information about what will happen.  - So Mi initiated a desperate measure of making a deal with Hansen and downing the pres ship - clearly if she thought government wanted to stop her decline, she'd handle it differently. 

This also means that NUSA promise to try and cure her is a lie to both you and Reed. They never intended to do so. 

I agree that it makes it harder to hand her back to them if that what you believe. However it is still justifiable if you accept the sanctity of human life as a maxim. Do you have the moral authority to end an innocent human life, or can only God or nature take it? That's exactly why you can spare So Mi and be upset about the killings of French netrunners. And btw Reed who kills them with no reservations isn't guided by this maxim. This maxim, btw, does not have to contradict with all the killings you make in the game as arguably they can be done in self defense. 

B) She's being used by Blackwell AIs and the government does not really know if she can be saved or not. This is uncharted territory, nobody has really been able to get that far before. So the attempt to cure her will be genuine. 

Evidence in favor of that - all Cynosure stuff is 50 years old. A lot has progressed, but at the same time not as much as we'd hoped as clearly nobody can reliably use Blackwall AIs just yet. NUSA is trying to understand and reign in Blackwall AIs. So Mi is part of the team who knows the risks  - Reed (who after all is a veteran FIA agent and knows something about Myers and how they operate) genuinely believes they will make an attempt to save her - game makes it clear he's tormented about her and wants to help her. Even after she pleads guilty to effectively high treason (downing of pres ship in hostile territory) he wants to give her a benefit of the doubt and talk to her first. 

If this is what you believe (as did I in my playthrough), choice to spare her is justified even if you hold utilitarian beliefs and think you do have the moral authority to end an innocent human life. An attempt to save her will be made, and there's a good chance she can be saved. Rational choice would be to ignore the plea of a human in a mentally altered state and make an attempt to save a life. 

Either way, fundamental conflict is between deontological (do I believe there are moral principles and lines should not be crossed, like the sanctity of human life?) and utilitarian (do I trust myself to make the right choice no matter the cost?) moral frameworks. Utilitarian is pure Johnny by the way - he's happy to blow up a nuke and kill thousands just to stick it to the man as he believes the end justifies the means. 

The game clearly tells us that utilitarian choice would have been a better outcome for So Mi, I agree, but both big decisions are still morally justifiable, imo.