It's just a figure of speech. It's a reference to Col. George Armstrong Custer, an infamous fame-seeker who chose to sacrifice himself and his men to fight an unwinnable battle on a hill at Little Bighorn that served little point and purpose. To "die on that hill" simply means you're stubbornly hanging onto a point, far past the point of relevance.
And listen, I totally understand your feelings regarding retroactive continuity. It's often implemented carelessly and can ruin some great universes for the sake of telling new stories. However, retconning is often a necessary evil when talking about persistent fictional universes. Just like completely disregarding continuity can be troublesome, stubbornly sticking to that continuity, and thus gimping your ability to tell the stories you want to tell, is even worse.
And whether you agree with it or not, the story of Peggy Carter and her ascension from lowly SSR agent to founder of SHIELD is a story certain forces at Marvel really want to tell. The One-Shot inspired them to do so, but they wanted to take that story and make it more detailed. Ideally, they could so without contradicting what happened. But the One-shot makes that difficult because it was never originally designed to have any holes that needed to be filled. So, they chose to simply overwrite it.
You're welcome to your opinion. I might have even agreed with you if you simply treated it as the tiny detail it is rather than some universe-breaking error. But retconning is a such a common practice that I just wonder why this one sticks out to you so much?