Why are Maki's action at the Zenin's headquarter viewed as act of villainy here?

Maki was about to be murdered. She received a powerup and faced her father in a kill or be killed situation. And the entire clan went all out to hunt her, there's no other choice but to kill if she wants to get out of there alive and she didn't even kill Naoya, the last man standing.

There's very little to suggest she has become "evil" or even went rogue. She'll regroup with Yuji and co, probably in the next few chapters.