The CIA wouldn't have fought Vought. They would have contracted them to make super agents.
I think (in the comics at least) the CIA was worried about National Defense relying on Supes when those Supes were almost universally incompetent pieces of shit and subject to blackmail.
There’s also the implication of an arms race, analogous to the Cold War, in which there’s a risk of a hostile nation developing a supe ‘better’ than Vought can. Glorious Seven Year Plan, the Soviet premier supe team, was a joke, but the risk was there for them to have a supe that could easily defeat Homelander.
At the end of the comics, Vought creates a new super team, The Pure, which are basically identical to the Seven and a number of second-rank heroes, and still have all the same flaws, right down to the new Deep still having to wear his helmet. This implies Vought’s ability to create supes is more limited than previously shown.
Plus, the CIA had access to a stabilized form of V, hence Hughie, Butcher and Frenchie using it to gain super-strength (Mother’s Milk and The Female already having superpowers) and Mallory gaining extended lifespan (with possible other abilities).
In my comics headcanon, Edgar and Butcher already have unusual forms of superpowers. Edgar is super-intelligent and completely immune to fear or panic, and Butcher has the ability to innately perceive personality flaws and motivations, which is why he’s so good at manipulating and blackmailing people. YMMV again.