While I do believe that Shinji was not at fault, even if he was, who in their right minds would confuse, threaten and piss off the key to humanity's destruction? That was just plain stupid. They had 14 years to sort out their feelings, yet they chose the worst 14 minutes to go on an outburst.

To put it simply, Misato and her crew underestimated Shinji. They did not think he would be able to escape their grasp, so they believed treating him like shit because of their uncontrolled emotions is alright. Yeah, that worked out just fine.