I think that Wille's treatment of Shinji was a mix of wanting to manage him, and fear about him.
Fear because what he could have become : they told him to never pilot an Eva again because somehow he have the ability to Awake them, and to drive their point him... they put him a DSS Choker, a device initially designed for Kaworu, an Angel. They also said that they don't trust him, trust him to do what? Stay put and don't get into an Eva, why would they even get concerned about that : he's a scrawny 14 years old boy in a completely alien situation and inside a giant battleship which he doesn't have any idea of the layout and full of trained soldiers, and they didn't even thought that neo-NERV could have any interest on him, so why the hell did they put him a DSS Choker? Just put in a cell and the job is down, he's no Solid Snake!
Did they feared that he could pull a NGE!Kaworu and gently float while mentally commanding an Eva to wreck havoc while generating an AT Field to protect himself until he reach the armored pod where EVA-01 is contained and finish what he started 14 years ago?
And what if it's exactly what they fear? Last time we saw Shinji, his eyes turned red(like Kaworu's) and he awoke his Eva and started an Impact(like Kaworu, an Angel could do). And his eyes started turning red a few seconds before his entry plug got all Technicolor, there is the possibility that after N3I Nerv recuperated the Eva's black box, examined the contents and witnessed this moment, wondering just what the fuck Shinji Ikari
really is.
Now about the debriefing, Misato, Ritsuko and Sakura clearly wanted to give him the informations slowly, where they screwed was in the order of the revelations :
First they told him where he is(AAA Wunder), where is EVA-01(serving as the Wunder's main engine) why he can't pilot(previous point plus his synch-rate now at 0.00%) then immediately continued by telling that since somehow he unconsciously briefly awoke EVA-01 in space, they put him a DSS Choker as a symbol of a "punishment" and the fact they don't trust him... why? Why wouldn't they trust him? From his point of view, last time they met he was saving their ass from being vaporized by Zeruel! And why punishing him by putting him a fucking collar bomb?!
And notice how Ritsuko diverts his questioning(why are you doing that?) by asking to Sakura to present herself, revealing the 14 years time skip.
Thankfully the diversion succeeded(well, that was a fairly big diversion) but still the 14 time skip has nothing to do about why they put a bomb around his neck and want to punish him. Asuka coming, triggering a reaction of joy and relief in Shinji continued to divert his attention, who diverted the topic on Rei, at which point Mark.09 attacks and ruin WILLE's chance to explain everything to Shinji and finally immunize him against Gendo's manipulations(something Gendo couldn't let pass of course!)
But for me that doesn't change the fact that they told him about the DSS Choker detonation function and it symbolizing his punishment and their mistrust in him, because that immediately antagonized him, Asuka throwing her tantrum and Misato telling him that "Rei is no more" only serving to enrage him even more, and finally ignoring him when Mark.09 attacked(albeit for good reasons, priorities in a warship and all like
thegoodson said) being the last straw that broke the camel's back, and prompted him to call for Rei and get out with her(his line "Enough!" just before he called for Rei wasn't chosen at random, he really is fed up with them making him feel unwanted)
The fact they diverted the topic when he asked why they are punishing him and don't trust him and showing it with a anti-Angel bomb is an hint that they wanted to give the revelations easily, little by little, but they wouldn't had to divert the topic if they didn't told him since the beginning that they are punishing and mistrusting him, when Shinji asked "what does it do", Ritsuko should have answered "it's a safety device that prevent Awakenings, a physical security for us, I will come back on that later", and told him about what he exactly do only after showing him what he did to deserve said punishment, be it because he destroyed the world, almost destroyed it but" thanks God that this fubking Angel was here to stop you but still you screwed up hard", or because they feared what he could have become after his experience inside EVA-01, or maybe some of these reasons at the same time.
And
only after that, tell him that because of this(these) reason(s), they can't take any risks/he must be punished, and that this Choker is here for that, and that if he does something stupid they can kill him with it, or it will kill him automatically if somehow he gets into an Eva and awakes it, because there is too much at stake. Then there is a good chance that he would have understand why they are acting the way they do.
Alas, 14 years living in a red wasteland and commandeering troops, making her little more than a soldier at heart, probably destroyed most of Misato's former tact to deal with children(not that said tact was fabulous to begin with...), and Ritsuko never had any tact to begin with, so maybe we could assume that both did their best with a situation they probably didn't face since Asuka and Mari turned (mentally) 18.
That and the fact Mark.09's fist going through the wall make this Idiot Ball moment of WILLE moot, so in the end that was an "aborted" Idiot Ball!
But an Idiot Ball nonetheless.