I think I see contempt and hurt in her eyes to be honest. I know she has other emotions for him but that's what I see at that moment, maybe a wee bit indifference too.
This. The middle one, at most
, might have some lingering pity if you squint, but that depends on where her eyebrow is and we don't see most of it. Could be just a generic 'hardened old person who is dead inside' expresson.
The first one is just strict or disdainful.
The last one is almost downright spiteful.
(Especially when coupled with... she must have known what that exact line would do to him. Anyone else, I wouldn't assume malice where stupidity or lack of ability suffices, but not Misato. She understands this exactly.
That said, the thing about Misato's emotional state is not that she has much of one feeling and little of another, but that both strong negative and strong positive feelings are present in comparable quantities, and she's actively trying to keep all of that volatile mixture under the lid so she can keep captaining her airship with some semblance of rationality.
Note how she leaves most of talking to the more calm Ritsuko who, while less cynical than her series or pre-timeskip self, is more capable of being cold and objective about it.
It might not be that much, or not only
Shinji himself as that he used to be a sort of 'morality chain' for her and expects her earlier, less pragmatic modus operandi to be in place, from back when she had time and ressources for the life of a single girl and the like. She probably didn't like
compromizing her ethics; It must have been a gradual, painful and frustrating process.
He's an inconvenient, ugly mirror of her past self.
In any case, it is noteworthy that we have a parallel to her introduction scene here. She first shows up with sunglasses, too. They mainly serve to make her look cool, but also set us up for a sort of 'reveal' when we first see the 'windows to her soul'.
In ep 1/ 1.11, this is a moment that obviously says, "Here is a token nice person, you can even call her by her first name!"
Q!Misato is probabl purposely kept aside/ambiguous at first, too, untill her eyes are 'revealed', and... yeah. At very least we can agree that they no longer look like they did in 1.11, however you chose to classify the present state.
I don't think Mitsuishi-san would've had such a "Wait, why is she saying things that will obviously make that kid uncooperative"-experience if she was told to play Misato that uber concerned. Struggling, and not entirely suceeding to fight back unwanted old emotions? Very obviously, that's how Shinji is even alive anymore. But "just pleasing her crew and secretly wanting to hug him" or "strict parent mode"? Seems like wishful thinking to me personally. The former is particularly ridiculous since Sakura & co practically worship the ground she walks on. No one would question it if she took a few minutes to speak with the prisoner one on one, or with just Sakura present.
"Please be very, very cold" indeed.
Alas poor Kaworu! I knew him well...