PSA: A clarification on the state of civilian rights in Leaf
It's come to our attention that there's been some unclear/contradictory information about civilian rights in Leaf. Please consider this an authoritative statement. If anything in past updates contradicts it, please assume that the characters misunderstood or miscommunicated the facts, or that the grue missed a spot.
Although there are technically laws protecting civilian lives on the books, actual protection for civilians comes from the existence of the Merchant Council, the body which regulates civilian trade and resource production in the Fire Country.
The MC is able to call an embargo which stops civilians from producing resources for, or providing services to, ninja. This would be a disaster for all ninja, since they do not do their own farming or crafting. However, it would also be a disaster for civilians, since many (if not all) ninja would resort to violence in order to obtain the resources they need. In addition, it would leave the village vulnerable to its enemies, meaning the Hokage would have to take extreme measures. It's never happened, so nobody knows what the extreme measures are, but they could range from executing and replacing the Merchant Council to total enslavement of the civilian population so something like this doesn't happen twice.
Thus, the MC is desperate not to find itself in a situation where an embargo is necessary. However, there are two circumstances which would force its hand.
1) The Hokage passes a law that threatens the entire civilian population. Allowing ninja to compete with civilians financially would be an example of such a law.
2) Ninja start killing civilians indiscriminately, and the Hokage fails to step in and stop them.
Murdering a single civilian will almost certainly not be enough to move the MC unless it was a very important civilian, such as a member of the Merchant Council. Murdering a small number, especially of undesirables such as six yakuza, probably won't either. However, the Hokage is aware that the MC could ruin the village if driven over the edge, and will not be impressed with anyone bringing them closer to that edge without a good reason. Between this and the fact that lowering the number of civilians is generally harmful to the village, a ninja who comes to the Hokage's attention through lots of wanton murder can expect to have a bad time.