Maybe I'm being bias since Puppet is my favorite character, but I can never see her as a villain, just a victim who had her entire life stolen from her, and all she really wants to do is help others who have suffered the same fate as her.
In all honesty I think Puppet/Charlie should have been the first helpful animatronic before Glamrock Freddy, and Roxanne Wolf. It should have been her guiding us on how to survive the other animatronics considering she should have known whar William Afton looked like therefore not mistaking other Night Guards for William.
I can never see Charlie as a villain, and wish there was a way to remove her from here.