I think it’s really important to remember that Steve’s perspective, coming in to Civil War, is still very heavily influenced by WWII. The movie calls back to this significantly in a few instances, and for good reason; WWII was a global clusterfuck. Governments made bad choices, some worse than others, and a lot of people died before alliances of nations bothered to get involved. Even the ‘good guys’ made the call to drop atomic weapons, which would be a recent discovery for Steve. He was shit at taking orders then, same as now, because Steve has always done what he personally saw as right, knowing that governments and councils might not make the moral call, or might wait too long to make it.
We see this when Tony busts out FDR’s fountain pens, apparently in some attempt to appeal to Steve’s nostalgia. But Steve has lived through the war those pens brought his country in to, and seen the far-reaching consequences of one man signing a document – it’s not something he can take lightly.
He’s still almost on board though, until Wanda being held in the compound comes up. And the word Steve uses then is very important:
The internment of American citizens of Japanese ancestry is not a distant memory to Steve; for him, it happened only a few years ago, and his friend and comrade-in-arms, Jim Morita, would probably have had family in internment camps. All supposedly for the greater good and safety of the nation. Steve balking and balking hard makes a lot of sense; even if Wanda is technically in a cushy situation, what happens when more enhanced people turn up? Ones Tony doesn’t have room for? What precedent is set for imprisoning them if he agrees to this?
Steve has always been about the individual right to choose what is moral. The kid who didn’t want to kill anybody, just stop the bullies, is the same guy who doesn’t want to sign over his will and his shield to others, to step in and follow orders given to him, regardless of what they are.
(Steve remembers all too clearly the acts of men just following orders.)