Mr Kaba, 24, died in Streatham Hill, south east London, after he was shot through an Audi car windscreen in September last year.
In the moments before the shooting, Kaba had driven into Kirkstall Gardens and collided with a marked police car.
The officer fired one shot and the musician in the head.
They have not been named publicly after an application for anonymity was granted in court.
Commissioner Sir Mark backed his marksmen and women protecting Londoners from terrorists and armed criminals, but said they are now worried how others may assess split-second decisions years after the event.
In a statement released on Friday: “I cannot talk about that case specifically as proceedings are very much active and I am mindful of the impact this is having on all those directly affected.
“On Thursday I met with 70 firearms officers to reflect on the events of this week.
“Like me, they understand the importance of transparency and accountability, and recognise the awful effect on everybody involved on the very rare occasions when lethal force is used by the police.
“That impact is exacerbated by the very slow speed that investigations, trials, inquests and hearings run at, meaning the lives of everyone affected are on hold for many years.
“They were understandably anxious as they consider how others may assess their split second decisions years after the event, with the luxury of as much time as they want to do this, and the effect this can have on them and their families.
“As I continue my work today, our firearms officers are on patrol deployed on proactive crime and counter terrorism operations as they are every day.
“They are not only prepared to confront the armed and dangerous to protect London’s communities but they do so recognising the uniquely intense and lengthy personal accountability they will face for their split-second operational decisions.
“Indeed, I understand why many of them are reflecting on the potential price of such weighty responsibilities.
“Bravery comes in many forms.
“When officers have the levels of uncertainty and worry I saw in my colleagues today, simply going in and doing their jobs not knowing what incidents are ahead of them is courageous.”
After being remanded in custody by Westminster Magistrates’ Court, NX121 later appeared at the Old Bailey for a second brief hearing to discuss bail.
He answered “yes” when asked by the court clerk if he is NX121, and passed a piece of paper to court staff with his date of birth on it.
Recorder of London Mark Lucraft KC told the marksman that a plea and trial preparation hearing will be listed for December 1, with a possible trial date of September 9 next year.
A hearing will take place at the same court on Friday next week to discuss a legal order that bans the identification of the officer.
NX121 was released on bail on the conditions that he lives at a named address, surrenders his passport and does not apply for international travel documents.