This time is different.
All of those examples you gave were examples of brainwashing - of Captain America not being in control - control he would later regain. Also, no one was ever really hurt by Cap in any of those stories.
By Nick Spencers own admission, the Captain were seeing in Secret Empire isnt going to willpower his way out of this, because the Cap we know ceased to exist - and that Captain America has done all manner of HORRIBLE things including bombing a city of 500,000 people, starving large parts of the US, building concentration camps, sanctioning public executions, and agreeing to vivisection.
During the read, Hydra-Cap was beginning to sense Elisa/Madam Hydra was manipulating him and an uprising plan by Faustus and Zola, ...could've led to Hydra-Cap to go through that 'Number one was a high level politician who set up an conspiracy to destroy peoples' values and ideals'. That destroys his faith in Hydra and Hydra-Cap uses the Cube to restore him to the original form.
I suppose this way, showed that Original Cap wasn't responsible for the killings, starvings and executions during the run.