Balancing different control types is something I've been thinking about recently, considering several approaches, but honestly all the ideas I've came up with have their cons. I'm using a HOTAs and mostly play PvE, though I've participated in some organic and training fights, and an organized PvP training.
So, you can stop the mouse at an (almost) instant, which stops any input. Releasing pressure on deflected joystick means it has to return to the center, and it will always take some time, depending on the centering method, and can even wobble if you literally just release the stick. So there are some drawbacks, but "fixing" - or balancing it - isn't that easy either.
Some approaches I've thought about include (yes, all have MAJOR drawbacks):
1) Flight simulator approach: some flight sims have that you simply can't use mouse to control aircraft at all, or it's not efficient and wonky, or servers can enforce usage of a controller. This would alienate and split playerbase.
2) Balancing approach: increase the micro-gimballing effect of fixed weapons. Enough to not need shooter-like pixel precision, but still need to manually aim at a target. This "balancing" could actually break the balance.
3) FPS/crossplay-style approach: ability to select what control types you want to instance with with. This literally breaks any sane way to instance and would cause problems with multiple simultaneous inputs (you can easily have controls mapped to a controller AND mouse+keyboard at the same time)
None of these seems very plausible, do they? What the game really needs is a complete rework/balancing on instancing, different career archetypes, crime & punishment etc. Even as a PvE player I'd be all for a single, big, Open-only universe, but that would also need rework on system security where High-sec systems are actually safe, but also and incentive to actually fight players in other ways than ganking and group wing fights.