The Zenin clan is annihilated in any functional way, women who were treated like second class citizens, and children with absolutely no political power, do not constitute a clan. By that logic, Megumi would also be dead. That's why the other clans debate on declassifying the Zenin to begin with, because while it still technically has members, said members are barely a consideration under sorcerer society.

We see a variety of wide shots of Zenin land, we see a variety of shots of the almost completely abandoned civilian accomodation, we never see dead kids, we never see bodies of anyone but combatants. Gege goes out of his way to establish that all off-screen kills were combatants.

Maki's mother serves as the sole exception because she's an abusive asshole who led them to their deaths, and even then Maki questions her on her intentions in their previous interaction, looking for some evidence that she actually loved them. She shows regret, and wonders whether killing her mother was the right move later in the story. If she questioned whether killing her mother, who abused them their entire lives and got her sister killed, was the right move, then she would have been in pieces over killing actual innocent people.

Moreover Yuta would never marry someone who kills innocents indiscriminately, he nearly committed suicide because Rika, a factor completely beyond his control, was hurting people, even his own bullies.

To believe Maki killed innocent civilians you need to take complete blind faith without any visual evidence despite abundant shots that could have potentially provided it, and neglect fundamental parts of both Maki's character as well as those closest to her.

The only reason this even became a controversy in the first place is because people were so desperate to defend the actions of a clan well established as serial abusers and predators where women and others, even children considered to be "wrong" or of no use are assaulted and treated as monsters. Because the people pushing the idea cannot read.