Well, that is classic but also a terrible cliche, says the Korean-English person. Le Carre is all very well, as is Slow Horses, but I’d like something different. Cynicism is boring, sometimes. The intelligence services act as the suspicion of the nation, but nations can aspire to become better. As I said earlier, I’d like a Bond I can root for, not someone who’s just yet another cog in the international murder machine.
It’s actually quite realistic that you’d want an active field agent to be able to make decisions of the fly, and while you would generally want them to prioritise the mission (whatever that may be) you would also want them to be able to make the best decision at the time, and that can include the morality and ethics of the situation. The history of intelligence and military operations is full of examples of when people who were supposed to obey orders without question did not in fact do so for moral reasons, to the greater good (or, in a few cases, to the survival of the species). Those people should be celebrated as heroes.
You wouldn’t want everyone to act like a Starfleet officer, as it were, but if you have one agent whose job it is to do the right thing and do it well, because he basically operates under a version of superheroic tropes (which cinematic Bond often does already) then you might want that chap to be able to change the plan as needed.
I’d think you’d have to make it clear in such a portrayal that M, Moneypenny, and Bond are quite exceptional to both the civil service and the intelligence services, and that many in the government might think their approach to be a dangerous liability, but as long as they keep on winning it’s hard to argue with. That would be an arc over several films.