The problem is the backdoors to SHIELD used by the oligarchs that want to give it secret orders are ultimately going to be used by HYDRA as well. In fact, one of the failures comes from the belief that the HYDRA element infiltrating SHIELD can be detected and cleaned out as if with an antivirus scan.

We've seen this the way NSA turned from a communications security department to a surveillance and intelligence department (that is, from anti-surveillance to surveillance), so instead of exposing and closing exploits and vulnerabilities, they catalogued them in secret for their own use -- leaving them available for other interests, including rival foreign states.

I'd like to say we have the terror scare from the 9/11/01 attacks to thank for that, but federal law enforcement in the US like FBI and NSA have secret-police tendencies, and like to use their powers to harass or neutralize enemies of the current administration, so this has been going on for some time.

A recent Behind the Bastards two-parter about How Capitalism Ate Christianity takes it as far back as the Great Depression and resentment of the New Deal. Larry Lessig notes that Boss Tweed in the 1850s was already moving to turn the US into a plutocrat-run autocracy, hence the current government as an oligarchy with small democratic features.