Why? Because the implications are obvious. Because in the past Jaina had always argued for peace and for diplomacy despite the border skirmishes for that very reason. I mean, seriously, how do you plan removing from power a group of people who are armed and very adept at combat, who are furthermore surrounded by an armed guard and by loyal adventurers? Do you think she expected them to come in quietly?
The threat of the Horde was ended. A horde led by Vol'jin, with Baine and Thrall and Lorthemar in the highest tier of leadership is a Horde that can be trusted enough not to risk more alliance lives. Jaina knows this. But her anger is so great that defeating the threat is not enough.
Thrall indeed bears guilt for all of Garrosh's actions. He acknowledges that much to Jaina, and it's the driving reason why he doesn't want to be trusted with power and defers to Vol'jin.Thrall was the jackass that put Garrosh in charge in the first place. Thrall is the piece of scum that sat on his ass while Garrosh unleashed a brutal war across two continents. Thrall twiddled his thumbs when Theramore was nuked to oblivion even when Jaina, his friend and comrade in battle against the Legion, the woman who sacrificed her own father for him, BEGGED him to stop Garrosh. Thrall is the hypocritial scumbag who only got off said green backside when his own precious orcs were about to get a well-deserved retaliation. Thrall was the dirtbag who refused to punish orcs responsible for the brutal murder of Night Elf Sentinels when he was still Warchief. Don't you dare call him some sort of paragon of peace.
But while Thrall was still ruling, during Wrath, he wasn't completely free to rule. Garrosh was already gathering a very powerful faction of young orcs, and even young tauren, who wanted more aggressive leadership. If he wanted to keep the peace with the Alliance, he had to keep the peace inside the Horde too, and that meant appeasing Garrosh's faction, which is why that went unpunished.
Btw, Thrall wasn't twiddling his thumbs while Garrosh did his thing during Cataclysm, he was trying to keep the world from collapsing on the plane of earth. And by the time MoP happens, he was too ridden with guilt, and too isolated within the Horde to act.
Jaina's anger towards Thrall is just, but it's excessive. Thrall should have foreseen what Garrosh would do, but instead he trusted he could appeal to his better nature, and make a redeemed Grom out of him. And Thrall could not just up and go when Jaina asked him, the rift between the plane of Azeroth and the plane of earth still had to be healed.
And this is what angers me the most. Jaina was a person who didn't judge people on a basis of character, but on a basis of circumstances. She knew that very often what people did was because of their circumstances, not because they were intrinsically evil or callous. For this, she was the voice of reason, the only one in Azeroth.
I had a noble, wise, brave and courageous hero. And blizzard turned her into a generic "and then she went crazy".