I believe Sharon Carter did that in the Steve Rogers Captain America book's tie-in to Secret Empire, calling HYDRA-Cap a fascist no better than the Red Skull, or something to that effect --- and both Captain America books were still being written by Nick Spencer while Secret Empire was happening, last I recall.
The spider is always on the hunt.
I just read Marvel Tales Knull #1 and it mentions SHIELD broke apart and then a Symbiote situation arose, but it’s very vague when that happened.
I’ve had a kind of another rethink about SHIELD recently, and it started like this.
SHIELD was a direct result of the unaccountability of superheroes to the normals. Up until 1965 in Strange Tales #135, when SHIELD was first announced, the superheroes acted independently, assisting all the government services, like cops, FBI, CIA, Fire Dept, and the Armed Forces. Nobody until then, questioned the help given by vigilantes, and just waved it off as good help. The appearance or revelation that a SHIELD organisation had been struck, is a direct result of the suspicion that one day the trust shown in vigilantes would deteriorate. That day came at the end of CW #7, when all the services gang-tackled Captain America hammering on Iron Man, the supplier of arms and tech to SHIELD (Tony Stark).
So, from my standpoint, SHIELD represents that suspicion that appeared in 1965 in the normal community. From 1961 - 1965, superheroes went through a golden era, which was suddenly cut short, and sent shivers through the superhero community because SHIELD cast a dark shadow over the superhero vigilantes, knowing the normals had now made a contingency for them, the vigilantes. SHIELD morphed into Cape Killers by 2006, and achieved its aim to reign in the superheroes.
Then that went pear-shaped when they gave power and authority to a known psychopathic murderer like Norman Osborn, just because he killed the leader of the Skrulls' Secret Invasion in full view of the media and the public, proving that for all the talk about making superheroes accountable to the public, S.H.I.E.L.D./H.A.M.M.E.R. was ultimately more corrupt and unaccountable than superheroes could dream of being. Not to mention, Bendis's Spider-Man: Miles Morales showed a lot of supervillains that were previously detained by S.H.I.E.L.D. getting released after Secret Empire because without S.H.I.E.L.D., the laws on the books no longer justified their detention and imprisonment, thus proving --- as if HYDRA-Cap taking over in Secret Empire wasn't enough --- that S.H.I.E.L.D. had been every bit as unaccountable and irresponsible with its power and authority as its leadership, particularly under Maria Hill, accused superheroes of being.
The spider is always on the hunt.
I suppose SHIELD got infected after the Initiative experiment and then with HAMMER and later Secret Empire. There was a limit to its effectiveness against superheroes, considering that experiment failed. Does SHIELD then still consider it has a role? Gen Ross and J Jonah Jameson will say yes.