I don't know, I think they could use a little more. Maybe something more physical to say the least.
Just for curiosity, is there a reason you always want everyone to get spanked?
Like sure they treated him like crap, I think even saying that they 'helped' him is going too far if one keeps context in mind ( Also Emotional meltdown reactions aren't conscious decisions & not hating someone quite enough to kill them in cold blood doesn't equal loving them)
The actions themselves are really not ok, but actions happen in context and that context is 14 years of apocalyptic hell compared to which the few months or so that they knew Shinji as a person are a fart.
Under these circumstances you can't really say that these actions, as bad as they are & as much as they hurt Shinji, and as much as he didn't deserve it (so get got played by Gendo. So did everyone, he was just the designated triggerpiece. He didn't even know this could happen.) under these circumstances they don't make Misato & co bad people
who deserve punishment. They're only realistic.
It's easy to be a saint in paradise but Misato & Asuka currently live in Hell... and have been the last thing standing beyond humanity & annihilation for years. They're by all means heroes, anti-heroes perhaps, but, from what we see WILLE's a lively organization & a star of hope and Misato is very much the creative & daring leader we knew her as. If you're just about any non-Shinji person, WILLE is great.
Ultimately all that is besides the point
tho: Regardless of how one does or doesn't read their actions, what would "punishment" solve, and what would it do for Shinji? How's such "an eye for an eye" logic remotely constructive? There's few humans left, anything WILLE has is a valuable ressource & insisting on "payment" won't help Shinji win back their respect. Wether he should
have to has little bearing on wether he will
have to if he dicedes that his goal is to get along with them.
It's kinda all in this exchange:
Shinji: "But I knew nothing about this, I was just trying to save Ayanami! I had nothing to do with this!"
Kaworu: "That may well be but that's not how the Lillim see it"
IThe fact that this clusterfuck happened and that they blame him is a reality he has to deal with somehow; To that effect
his side of the story is kinda secondary at first.
...As for Shinji, I doubt he blames them after he saw the city. He was understandably confused & frustrated but at this point he mainly blames himself. Not that when they descend to terminal dogma he's like "all of Misato & the others' hard work went to waste..." when he beholds the state of Lillith. He tried to talk with Asuka & the most he did was throw her out of range; Though to some extent it was a mutual communication fail on all fronts.