The behaviour of 'emergency brake when called' is arguably quite realistic because there are a lot of drivers today who jam on the brakes when they get distracted by anything from young ladies to the side of the road, an incoming sms, a dropped french fry, accident on another road 1/4 mile away... etc etc
As for whether joysticks work in STO - they do but they are over sensitive and you need a joy2key mapping software to do the key/button assignments.
An Xbox controller is much easier to use actually.
This is important because a lot of players don't realize you can turn off that "stop when pop-up appears" system in the game.
However the alternative is:
Crash into, or fly past, all large objects.
Still have a backlog of Sector Traffic Control popups.
Get stuck before your destination.
If you fly past several sector borders, the popups will stack up. Upon reaching your destination, if you click the pop up on the screen to travel, it will actually take you all the way back to the first sector you passed.
The on/off option in the options menu is simply trading one bad option for another.