I know I've said it before, but here's my take on Horizon (using my Shep specifically).
Shepard has been - not so discreetly - trying to unturn Kaidan for some time when TIM tells us that Horizon is under attack and Kaidan is there. Heading there, with this informaiton, she's a mad woman (and I mean that as both angry and crazy). As a Vanguard, she's always a bit reckless it seems in her attacks, but she's even more so now, because she feels this push that she has to find him before its too late. It's driving her forward, to reckless abandon.
When they finally drive off the Collectors, and that ship takes off, she's seen no trace of him on the colony, and if he were really there, what if he was one of the many just abducted? Her mind is literally still racing with the countless numbers of possibilities of what happened to him when he finally shows up.
And then it's just "It's him. He's ok. Everything's going to be alright."
So, when he finally adjusts to the fact that she's really there and the awkward conversation begins, she has not managed to get her bearings, and she's completely thrown by his reaction. And then devestated, and it is taking everything for her to maintain her composure. After all, she's still on the field, in front of her squad. She has to be Commander Shepard there. Not Alexis, Kaidan's ex-lover. So, bad dialogue and all, that's how things play out for them.
Yes, she can understand where he is coming from, but she does not accept it and it hurts her. Plus, it still makes her angry. And, the email ends up making it worse for her when it comes along.
Now, I, as a player, agree with Kaidan's reaction, believe it to be IC, and have no problem with it. But I am not my Shepard. I, as a player, dislike some of the dialogue that Shepard gets on Horizon (there are some very good options you can choose though), but I feel that it can accurately show things for my Shepard. I had to have a few playthroughs and really think about it before I came to full terms with it, but that's where I am now regarding Horizon.