tbh most of the horde didnt want garrosh to have it eitherI believe she was trying to keep a dangerous weapon out of the hands of a mad man, Darnassus wasn't going to be using that. Neutral organizations exist for the good of the world, that's why they usually stay out of horde and alliance conflicts and only work against true threats.
The guards I don't know about, I don't know why they were standing in front of the stairs in battle position either. I don't know why Aethas didn't even seem to care when she killed three of them. She asked Aethas to leave, and he refused, in kind of an arrogant way (I don't know if that was intended but that's how it came across with the voice acting). So he was imprisoned because Jaina doesn't want Garrosh's influence in the city, and the Sunreavers have helped him yet again.