Presumably Hank Henshaw didn't just now get turned into a cyborg. He's obviously been one for some time. So why has he been just hiding out at Cadmus for all these years instead of exposing J'onn as an impostor? Why wait until now to show himself?
I have several thoughts on that:
1) The DEO clearly had/has the official sanction and support of President Marsdin and presumably others within her administration/cabinet, and likely had the official sanction and support of whomever held the office before her
2) The impression I got from Col. Harper is that, prior to revealing themselves to the world, Cadmus was an extremely covert "black-ops" branch of the US government and one that may not have gotten the same amount of support as the DEO, possibly on account of being seen as too "extreme"
3) It might not have been advantageous for Cadmus to reveal what they knew precisely because of the DEO and Henshaw having full Presidential support and sanction, and any claims they made against Henshaw might've been dismissed