Exactly what do you think is he being ordered not to run away from? From doing his job which only he can do and the world depends on? Of course they would order him to do that even though they're being hypocrites by doing so. Except, as I pointed out in my last post, they DO at times admit to being hypocritical and accept that it's Shinji's choice and if he doesn't want to there's nothing they can do to stop him.
The situation's still constructed in a way to where Shinji will be in the wrong regardless of what he does. Also, I recall that the only person who actually says that Shinji actually has a choice (where he really doesn't) without trying to guilt-trip Shinji is Kaji.
Anytime Shinji actually is going to develop in a direction that's remotely positive, the plot pulls the rug out from under his feet and forces him back onto square one. It would be truly sad if it wasn't so predictable or hilariously contrived. It probably comes with the territory concerning these pseudo-tragic stories about failure and etc, but I've never seen another series that was so ham-fisted and annoying about it.
I'll admit that there is a personal frustration present because I do genuinely like Shinji as a character (unlike a lot of anime/mecha fans). I want to see Shinji grow stronger (acknowledging that he's already strong in a lot of ways), I want to see him overcome his obstacles, and finally decide that he's got nothing to run from and discover that what he was looking for was there all along. That all sounds cheesy and it probably is, but so what? Blame the story for making Shinji into a character that I can relate to and care about.
Yet, its Shinji who the story presents as being in the wrong. He's wrong whether it's for telling Nerv to screw-off and leaving the organization that blackmailed him; wrong for calling out his father on his unethical and dumb actions; wrong for
Don't confuse the characters doing things for Anno considering what they do as acceptable behavior. The double-standard IS the point. Their psychological damage will not allow them to act in the way that would be best for everyone including themselves. In other anime, if one character is feeling bad or unsure of themselves, they will randomly realize the error of their ways or be broken out of it by a simple inspiring speech. NGE mocks this, pointing out both that it's not that easy to snap out of such traumatizing things and that even if it were it's unlikely any of the people around you are going to be in a good position to help you do that. NGE is a character study of hypocritical, fucked up people, which coincidentally is what real life is often full of. What's wrong with that?
I get that NGE is the study of broken and screw-up people and this does correlate with real life. What I don't like is that this essentially keeps characters stuck on square one which is counter-intuitive to story telling where characters change and develop overtime and is also laughably unrealistic with real life. It's about the same as a common criticism of Freud where he got most of his findings from studying mentally-ill patients. The findings are interesting to study, but the results aren't universally applicable to most people.
I get that these characters all need therapy and I do sympathize with folk like Shinji and even Misato despite my hang-ups about their characters. But just like real-life, there comes a time when an individual needs to nut-up, shut-up and do something. They can't just hang on to their problems and expect no one to call bs on it. They can't just stay in square one and not get right criticized for their inability to move-on.
If these were really organic characters then they'd change and develop like them. Misato admits that she's a bad guardian, but never does anything to correct her mistakes like tell Asuka to stop acting like a bitch or actively taking responsibility. Instead, she lets her own problems keep her from helping Shinji and Asuka during the times when they need her most. Maybe that's the point, but don't expect me not to hold Misato accountable.
I mean, can you imagine how much Misato's speech to Shinji in EOE would've helped the kid if it was said to him before his despair event horizon? Instead, it's too little and too late and whatever help that it might've had is immediately negated by Misato's kiss and the plot contriving Shinji to fail yet again.
Perhaps the double-standard is the point, but I've just seen it done much better than in Evangelion. It also doesn't excuse the characters for making easily avoidable mistakes or doing stupid actions that only pay off because the plot says that it does. (looking at you Gendo)