The Menenzes case wasn't questionable at all.
The problems with that case was more to do with what happened afterwards than what happened before.
The Armed officers had reason (Multiple reasons in fact) to suspect him. That all those reasons turned out to have innocent explanations was something that was only appreciated in hindsight.
There is only one way to stop a suspected suicide bomber and that is to kill him quickly, without warning, and in a highly specific manner.
If you shoot a suspect and he turns out to be innocent, you have killed 1 person. If you hesitate and he is in fact a suicide bomber you might end up killing dozens.
Sadly, public safety demands that the correct course of action is to shoot first and say sorry afterwards if necessary. If you are not shooting the occasional innocent suspect, then you are not doing it right.
I'm by no means questioning what the firearms officers did, i would clear them in court had i been there, they were acting on misinformation which led them to a reasonable beleif he had a bomb and intended to use it, and as you say the technical requirements of public safety meant shooting him 7 times in the head was the correct decision for them to make at the time.
Now whoever told them he had a bomb has some explaining to do i will admit.
What i'm asking, is if you say you cannot morally justify an institution that kills people (ie execution of murderers who have been convicted without reasonable doubt in court) because mistakes may lead to an innocent person being killed then how can you justify an institution that kills people (ie the armed police) with not only the potential, but a track record of killing people who were innocent and who, if it had been to trial, would have been cleared completely?
I accept that "innocent people might die" as a valid argument against execution, what i'm asking is how you justify "lawful killing" used to kill both guilty and innocent people at the same time. The end result of both scenarios is the same-mostly guilty people will die, but some innocents may die.