@Rafin
There's no retcon here, we're simply clarifying and reminding y'all because it's relevant now and there seemed to be some confusion. (Okay, we made one mistake: In the latest post we said there aren't laws on the books about this but there actually are. That's an irrelevant detail and we'll edit it out.)
De iure, civilians have a right to life, killing one will get a ninja executed, and if the ninja isn't executed then an embargo will be called that will force the ninja to bow to the civilians.
De facto, the Hokage doesn't want to execute his ninja and the Merchant Council doesn't want to escalate things with the ninja since that is definitely going to end in blood on the ground. It's an open question whether they could pull off an embargo, since it requires all the civilians to cooperate even when ninja start executing people -- which they absolutely would. It would be an incredibly chaotic situation and a lot of people would end up hurt, ninja and civilians alike. No one knows exactly what would happen and no one wants to risk finding out, so the Merchant Council isn't going to call an embargo unless it's absolutely essential.
How does that all shake out? Ninja bully civilians all the time but they usually don't kill them and if they do then they cover up the murders in order to maintain plausible deniability. At the same time, no civilian feels completely safe even in broad daylight, because a judge could deem "he fell on my kunai" plausible rather than execute a high-value ninja for the sake of a low-value civilian. This is well supported by evidence in the text.
Even beyond that, no one gives much of a toss about criminals so Asuma isn't that concerned that Haru killed a half dozen Yakuza, as it hasn't caused an issue yet and isn't likely to in the near future. If Haru keeps killing, or if he starts killing non-Yakuza, then it might cause a problem so Asuma wants Haru to stop.
As to the rest:
Yes, Hashirama enforced a 'no killing civilians' rule. Yes, those laws are technically still on the books even though no one really cares in practice. Yes, this level of protection, paper thin as it is, is still better than civilians get in most other places. Yes, the threat of embargo is the main reason that ninja don't use magic for economic purposes, since that's the one thing that almost certainly would get an embargo called. Other reasons include a culture of military service that says doing non-military things is shameful for a ninja, which is why people like Reo, Mai, and Atomu are so desperate to find productive and military-related work.