I think I can explain how Shepard reacts to Liara. I was thinking about it a little more, and it just hit me. Let me know if you think it fits. Now, before you say, we should know everything Shepard knows, and should be able to do/act whatever/however we want. Think about it, we can't really. There has to be some controls over the game. Some things we just can't do. I could list cases of these and reasons as to why, but that's not the point here. This is just the sad case of one, that really stands out. Thus our being upset over the whole thing.
So much attention was placed on Liara, that we forgot about Shepard. I think that's kind of natural because we are Shepard. We tend to think of our actions in the context that we are making the choices and have the control. The game however, expects us to understand what's going on, and for our actions to be based from this. If you don't fully understand what is happening, then you can miss the reason for what's happening and why, and your actions can seem out of place. Shepard might be us, but Shepard is still Shepard, in that, there is something that makes Shepard the person they are. The way things are said, some actions picked for us, as in not allowing us to make weird and abnormal choices. To try and understand, we have to accept that sometimes we can't do what we want, because it's not a choice, there is only one path. We don't always like the path, but that is what is laid out for us. The goes beyond the simple, as in, Liara can't come with us, because Liara can't come with us, because the game won't allow it, because she needs to be alive for everyone.
Ok, I'm rambling a bit, but I hope you all understand what I was trying to say there. Now, back to why Shepard reacts to Liara in the reunion. If we think about Liara:
She had just lost her mother to the Reapers, and likely was with Shepard when killing her.
She was forced to leave Shepard on the Normandy, by Shepard.
She was forced to watch Shepard die, unable to do anything about it.
She was forced to go out on her own to find Shepard's body, to lay her loved one to a proper rest, because no one else would.
While doing so, she was forced to take that body from the Shadow Broker, because he was going to sell it to the Collectors.
While getting Shepard back, we are told she nearly dies herself, and was forced to leave the only person willing to help her get Shepard back, behind to be killed or worse.
She has Shepard back but she isn't given the peace she was after for her and Shepard, instead she is forced to make a deal with TIM, to allow Shepard to be rebuilt. She can't let go, so she turns Shepard over and allows it all to happen, knowing full well the kind of evil things this group has done in the past.
She sits in her office for two years, worried everyday what will become of Shepard. What will TIM do to Shepard, will Shepard hate her now. These and many more questions go thru her mind for all that time.
She is forced to become a person that isn't her, while she might enjoy the work itself, as it reminds her of the old days, she is being a person she doesn't like. Anyone that truthfully knows Liara, knows this isn't her.
There is also the unknown reason for which Liara is forced to once again, let Shepard go. Unable to run off to the Normandy and leave everything behind, to find comfort in the arms of her loved one. Is it fear, for what Shepard might now be, is it fear of being hated and unforgiven, is it some deal we don't know about. Whatever it is, it must weigh heavily on Liara, to keep her from the only thing that has kept her going for two years, the one she loves.
Now, Shepard isn't stupid, and while we might not pick up all this, Shepard can from talking with, and watching Liara, in her office. Remember, Shepard fully understand Liara, they are connected with a bond that goes far beyond, even a lifetime of living together. They both fully understand each other, and I like to think, share a connection, that allows them to even feel what the other does. Liara says the bond transcends time and space. So think about this from Shepard's point of view.
What do you say to Liara, when she tells you she couldn't let you go. Here is the important part. Shepard did let Liara go. Shepard told Liara to leave the Normandy, and Shepard stayed behind, to play hero and save Joker. This is all Shepard's fault. And Shepard has had ever since waking up and till getting to Illium to think about this fact.
Upon seeing what this has done to Liara, and everything she had to go thru, because you had to play hero and save a fool. It becomes perfectly understandable that Shepard is a bit stunned and at a loss for words. Kind of out of character for Shepard to be at a loss for words. But if Liara is your LI, then you understand it would be cruel to tell Liara, you couldn't let her go either, because you already did, and Liara would have every right to yell at you for saying that to her. If you aren't her LI, then perhaps you fall for her at that very moment, and what do you say to her, after she just opened her heart to you.
Shepard has to feel all the guilt and pain, and sadness that Liara does now. It is Shepard's fault Liara went thru so much. Every bit of it. Shepard is stunned at the love Liara has, and then in that same moment, feels horrible for not going with Liara back on the Normandy. Shepard was a fool to save Joker and put Liara thru all this. Would it be fair to put Liara thru it a second time.
Anything affectionate at this moment, would be cruel, because no matter what, Shepard is getting up out of that chair, getting back on the Normandy, and running off to play hero again. We can't stop it. It's just who Shepard is. And it's very likely, that Shepard isn't coming back. You want to tell Liara you love her, then leave her again, and go off to die, all because you can't drop everything and be with her.
I think, while we might not like it, Shepard knows best, and doesn't have the big reunion we all want, because of what must happen next, Shepard has to leave Liara alone again, and maybe die yet again. To let her go, when she couldn't let you go. How terrible this must make Shepard feel. It's only fair to walk out that door like Shepard does.
This puts the picture scene into better context, as it shows Shepard thinking about Liara, and this is why Shepard must not fail, not for the mission, not for the preservation of self, but for Liara. Shepard has something to come back to, and a reason to live, because Liara is waiting and needs that reunion she was denied.
This is the troubled second act. Love is cast aside, for the mission. It's sad, it's painful, and it's not fair. The galaxy will burn, as will the one Shepard loves, if they fail. The many years it might take for the Reapers to return, it might not effect most people, but Liara will live long enough, they are coming and that's why Shepard must do this.