As presented here, I will agree with you. It felt especially weird to not omit it but to have it and switch it to Hydra. I think if they had just shown them storm the Red Skull's base it would have been OK. To show people "Sieg, Heil"-ing to Hydra was what was off.
Yeah, now that I've seen the short in question, I see it's more drastically revisionist than I realized.
From what I've heard, they're following the structure of the early issues of the
Avengers comic. The preview for next week's episode indicates that it's basically the same premise as the first issue of
Avengers, and the current team make-up is the same one the comic began with. Cap didn't join the team until issue 3.
I caught the premiere of this 2-parter at New York Comic-Con, but seeing it more clearly, and after seeing all the micro-episodes, makes a number of things clearer. For one thing, it's clear to me that this pilot would be difficult to follow without having seen the micro-episodes first. For instance, when I saw it the first time, before having seen the last few micros, I didn't understand that the Big House was a miniaturized prison inside the SHIELD Helicarrier. And I didn't realize the guy in the lab coat was supposed to be Hank Pym until he shrank down (I'd seen the first Ant-Man micro-ep, but I didn't remember the character design). He wasn't adequately introduced within the episode itself.
And that's a bad way of doing things. The core work should always be comprehensible on its own without needing peripheral works to explain it. Peripheral material should contain bonus information, not essential information.