I always thought one of the main shortcomings of the Dominator was how it is so darn slow at getting it to do anything. If the target were running around or running through a bunch of bystanders, the user could easily miss or explode the wrong person. It would be more efficient if it let you set it to the stun mode, shoot as much as you need, and then sort the people out afterwards.
While that would make better sense, the Sybil system doesn't care about user safety (especially as evidenced by a certain fratricide incident). Situational awareness is only as important as the characteristics they need to determine crime coefficient. An individual who could stun on their own will is a radical to Sybil as they no longer are under central control. Power is more important than results in that world, as it is assumed that as long as power is consistent, all issues are short term problems that can eventually be solved by tightening control.
We kind of see a similar situation in real life. Politics and political correctness (or whatever arbitrary measure of virtue is popular at the time) ends up micromanaging law enforcement or military and the individual initiative is removed. Even if the outcome from following strict orders results in terrible consequences, all failures can be forgiven so long as the powers that be were the ones that ordered the outcome. Written law becomes just a guideline, and people are just extensions of someone else's will who is not and never will be directly influenced by the situation at hand. The individual is sacrificed for the supposed common welfare.
Well, to what I see, it's not quite what you said.
For once, the system does grant Tsunemori's request to unlock and keep the Dominator locked on stun mode at the end of the first season. And she was an irregular, not radical. Then, when it got into Kougami's hands, it stayed the same as requested. Meaning the system do indeed make more than just one exception.
The same goes with law and law enforcements. If the result of an order isn't fit the situation, the field get a certain range of freedom on what to do. Depends on the result of their choice, they might be sung heroes instead of order breakers.
But I do agree that the problem is not about having the Dominators stay on stun at all time. We did see how a seeing people shot with Dominator (be it stun or emilinator): their crime coefficient goes up. Often into range of a latent criminal for a normal person. However it may become of the victims who got shot, it'll be a big problem for the public safety. Thus Dominators requiring clear shots is a must if the system wants to run properly.