The failure of the Red Skull's convoluted scheme to turn Steve Rogers into the instrument of his ultimate triumph was entirely baked in from the very start. The Steve Rogers who Kobik rewrote to become "the best (Hydra) version of himself" was - never - an agent of the real Hydra and was - never - loyal to Hydra's real ideals. Instead, he was the loyal agent of the entirely fictional, fairy-tale version of Hydra that Red Skull invented to appeal to Kobik's childish sensibilities. That Hydra was led by brave, self-sacrificing and heroic people who could do terrible things only because they had the best interests of humanity at heart, not megalomaniacal Nazi racists who just wanted to inflame and exploit humanity's worst instincts for personal gain. The rewritten Captain America was always going to be just as opposed to the Red Skull's ideology as the genuine Steve Rogers, only for very different reasons, and thanks to the rewrite, the 'Stevil' version was more than willing to kill to defend the honour of his fictional Hydra. At the end of the day, the mythical Hydra that 'Stevil' thought he belonged to and wanted to recreate in the real world simply didn't (and couldn't) exist without a wholesale Cosmic Cube-powered rewriting of everyone else's reality to match Stevil's verging-on-the-innocent faith in Hydra as a Good Thing, and it was the continued failure of the real Hydra and its real leaders to live up to the standards of Kobik's fictional Hydra that drove 'Stevil' mad with frustration.
With the recent reveal of how the Allies seemingly had to cheat in order to win World War II everyone is in a rage and anger as to how that could possibly be right and how it seems to fly in the face of everything Captain America.... except THAT'S THE POINT. Red Skull wanted Steve to be on HYDRA's side and thus when he made Kobik reformat Steve's mind this included his history in World War II which is, you guessed it, a complete insult to the sacrifices and bravery of the people who did fight on that day.
Although Skull instigated the act, the finer details of the changes is up to Kobik's initiative in fulfilling it. So it's less in character for him being irreverent, and more a naive her acting at face value knowledge. It's disrespectful because she doesn't know any better, not because he does.
There was a conflict at Civil War II about an inhuman who can show visions of the future. Carol Danvers wanted to use it for Precrime Arrest of the villains in said visions, and Tony Stark said that those visions were only possible futures, which may or may not take place as seen, or even at all. In one of those visions Miles Morales had killed Captain America at Washington DC. During this story, the context and build-up to that fight is clear, and the fight itself take place. But, in the end, Morales can not go further and does not kill. Corollary: TONY STARK WAS RIGHT!
Fridge Logic
Jane Foster had to be taken out of the combat field midfight in the middle of Secret Empire #9 because the Thor enchantment broke as she was not holding Mjolnir, and actually had not for a while — but in Secret Empire #10, when Good Cap finishes beating up Hydra Cap with Mjolnir, he hands her the hammer, and she's in Thor form again. How did that happen? note http://imgur.com/a/1kSQX
