That's all very nice and it makes sense given the time in which the film was made, but it still doesn't make it right.
I actually understand where you're coming from. I'm the same way with Cap comics (pre-Heroes Reborn anyway) and I did cringe a bit when TFA revealed that the Red Skull had a preliminary version of the supersoldier serum in his veins.
But to me a lot of "source material sins" are attoned for when the new take is still cool. And having the RS punch a dent in Steve's first shield and duke it out with him for an extended period of time at the end of the film made for some really exciting moments.
On the flip side Whedon's take on Cap really didn't defy any of Cap's established comic history but he had to give him that damn derpy cowl.
So at the end of the day:
Liberties presented in a cool way > sticking exactly to the comics in a derpy way.
And Jack killing Keaton's parents was cool.